From 14c14ac0fd1811c9ee22b51f501a5a66b279e509 Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Fri, 9 Aug 2013 18:34:33 +0900 Subject: [PATCH] Imported Upstream version 0.7.3 --- MANIFEST.in | 5 +- PKG-INFO | 6 +- distribute_setup.py | 107 +- pysam.egg-info/PKG-INFO | 6 +- pysam.egg-info/SOURCES.txt | 8 + pysam.egg-info/requires.txt | 2 +- pysam.egg-info/top_level.txt | 4 - pysam/__init__.py | 5 +- pysam/alternatives.py | 82 + pysam/ctabix.c | 3822 ++++++------ pysam/ctabix.pyx | 2 +- pysam/cvcf.c | 10447 ++++++++++++++++++--------------- pysam/cvcf.pyx | 4 +- pysam/version.py | 2 +- setup.py | 36 +- tabix/bedidx.c | 156 + tabix/bgzf.c | 555 ++ tabix/bgzip.c | 206 + tabix/index.c | 967 +++ tabix/knetfile.c | 632 ++ tabix/kstring.c | 165 + tests/example_btag.bam | Bin 0 -> 771 bytes tests/pysam_test.py | 10 + 23 files changed, 10486 insertions(+), 6743 deletions(-) create mode 100644 pysam/alternatives.py create mode 100644 tabix/bedidx.c create mode 100644 tabix/bgzf.c create mode 100644 tabix/bgzip.c create mode 100644 tabix/index.c create mode 100644 tabix/knetfile.c create mode 100644 tabix/kstring.c create mode 100644 tests/example_btag.bam diff --git a/MANIFEST.in b/MANIFEST.in index f613856..a0c9889 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -21,9 +21,12 @@ include pysam/TabProxies.pxd include pysam/cvcf.pyx include pysam/cvcf.pxd include pysam/cvcf.c +include pysam/*.c +include pysam/*.h include pysam/pysam_util.h include samtools/*.h include samtools/*/*.h +include tabix/*.c include tabix/*.h # pysam tests @@ -44,6 +47,7 @@ include tests/example.py include tests/pysam_test.py include tests/segfault_tests.py include tests/example_*.sam +include tests/example_btag.bam include tests/tag_bug.bam include tests/example.vcf40 include tests/example_empty_header.bam @@ -56,4 +60,3 @@ include tests/example.gtf.gz.tbi include tests/example.bed.gz include tests/example.bed.gz.tbi include tests/vcf-examples/*.vcf - diff --git a/PKG-INFO b/PKG-INFO index cc28edb..905bd25 100644 --- a/PKG-INFO +++ b/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 1.1 Name: pysam -Version: 0.7.2 +Version: 0.7.3 Summary: pysam Home-page: http://code.google.com/p/pysam/ Author: Andreas Heger @@ -11,8 +11,6 @@ Description: pysam ***** - For more information, see http://code.google.com/p/pysam. - Platform: ALL -Requires: cython (>=0.16) +Requires: cython (>=0.17) diff --git a/distribute_setup.py b/distribute_setup.py index b204902..a1cc2a1 100644 --- a/distribute_setup.py +++ b/distribute_setup.py @@ -14,11 +14,14 @@ the appropriate options to ``use_setuptools()``. This file can also be run as a script to install or upgrade setuptools. """ import os +import shutil import sys import time import fnmatch import tempfile import tarfile +import optparse + from distutils import log try: @@ -46,7 +49,7 @@ except ImportError: args = [quote(arg) for arg in args] return os.spawnl(os.P_WAIT, sys.executable, *args) == 0 -DEFAULT_VERSION = "0.6.24" +DEFAULT_VERSION = "0.6.34" DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/" SETUPTOOLS_FAKED_VERSION = "0.6c11" @@ -63,7 +66,7 @@ Description: xxx """ % SETUPTOOLS_FAKED_VERSION -def _install(tarball): +def _install(tarball, install_args=()): # extracting the tarball tmpdir = tempfile.mkdtemp() log.warn('Extracting in %s', tmpdir) @@ -81,11 +84,14 @@ def _install(tarball): # installing log.warn('Installing Distribute') - if not _python_cmd('setup.py', 'install'): + if not _python_cmd('setup.py', 'install', *install_args): log.warn('Something went wrong during the installation.') log.warn('See the error message above.') + # exitcode will be 2 + return 2 finally: os.chdir(old_wd) + shutil.rmtree(tmpdir) def _build_egg(egg, tarball, to_dir): @@ -110,6 +116,7 @@ def _build_egg(egg, tarball, to_dir): finally: os.chdir(old_wd) + shutil.rmtree(tmpdir) # returning the result log.warn(egg) if not os.path.exists(egg): @@ -144,7 +151,7 @@ def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, except ImportError: return _do_download(version, download_base, to_dir, download_delay) try: - pkg_resources.require("distribute>="+version) + pkg_resources.require("distribute>=" + version) return except pkg_resources.VersionConflict: e = sys.exc_info()[1] @@ -167,6 +174,7 @@ def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, if not no_fake: _create_fake_setuptools_pkg_info(to_dir) + def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir, delay=15): """Download distribute from a specified location and return its filename @@ -203,6 +211,7 @@ def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL, dst.close() return os.path.realpath(saveto) + def _no_sandbox(function): def __no_sandbox(*args, **kw): try: @@ -227,9 +236,12 @@ def _no_sandbox(function): return __no_sandbox + def _patch_file(path, content): """Will backup the file then patch it""" - existing_content = open(path).read() + f = open(path) + existing_content = f.read() + f.close() if existing_content == content: # already patched log.warn('Already patched.') @@ -245,15 +257,21 @@ def _patch_file(path, content): _patch_file = _no_sandbox(_patch_file) + def _same_content(path, content): - return open(path).read() == content + f = open(path) + existing_content = f.read() + f.close() + return existing_content == content + def _rename_path(path): new_name = path + '.OLD.%s' % time.time() - log.warn('Renaming %s into %s', path, new_name) + log.warn('Renaming %s to %s', path, new_name) os.rename(path, new_name) return new_name + def _remove_flat_installation(placeholder): if not os.path.isdir(placeholder): log.warn('Unkown installation at %s', placeholder) @@ -267,7 +285,7 @@ def _remove_flat_installation(placeholder): log.warn('Could not locate setuptools*.egg-info') return - log.warn('Removing elements out of the way...') + log.warn('Moving elements out of the way...') pkg_info = os.path.join(placeholder, file) if os.path.isdir(pkg_info): patched = _patch_egg_dir(pkg_info) @@ -289,11 +307,13 @@ def _remove_flat_installation(placeholder): _remove_flat_installation = _no_sandbox(_remove_flat_installation) + def _after_install(dist): log.warn('After install bootstrap.') placeholder = dist.get_command_obj('install').install_purelib _create_fake_setuptools_pkg_info(placeholder) + def _create_fake_setuptools_pkg_info(placeholder): if not placeholder or not os.path.exists(placeholder): log.warn('Could not find the install location') @@ -307,7 +327,11 @@ def _create_fake_setuptools_pkg_info(placeholder): return log.warn('Creating %s', pkg_info) - f = open(pkg_info, 'w') + try: + f = open(pkg_info, 'w') + except EnvironmentError: + log.warn("Don't have permissions to write %s, skipping", pkg_info) + return try: f.write(SETUPTOOLS_PKG_INFO) finally: @@ -321,7 +345,10 @@ def _create_fake_setuptools_pkg_info(placeholder): finally: f.close() -_create_fake_setuptools_pkg_info = _no_sandbox(_create_fake_setuptools_pkg_info) +_create_fake_setuptools_pkg_info = _no_sandbox( + _create_fake_setuptools_pkg_info +) + def _patch_egg_dir(path): # let's check if it's already patched @@ -343,6 +370,7 @@ def _patch_egg_dir(path): _patch_egg_dir = _no_sandbox(_patch_egg_dir) + def _before_install(): log.warn('Before install bootstrap.') _fake_setuptools() @@ -351,7 +379,7 @@ def _before_install(): def _under_prefix(location): if 'install' not in sys.argv: return True - args = sys.argv[sys.argv.index('install')+1:] + args = sys.argv[sys.argv.index('install') + 1:] for index, arg in enumerate(args): for option in ('--root', '--prefix'): if arg.startswith('%s=' % option): @@ -359,7 +387,7 @@ def _under_prefix(location): return location.startswith(top_dir) elif arg == option: if len(args) > index: - top_dir = args[index+1] + top_dir = args[index + 1] return location.startswith(top_dir) if arg == '--user' and USER_SITE is not None: return location.startswith(USER_SITE) @@ -376,11 +404,14 @@ def _fake_setuptools(): return ws = pkg_resources.working_set try: - setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools', - replacement=False)) + setuptools_dist = ws.find( + pkg_resources.Requirement.parse('setuptools', replacement=False) + ) except TypeError: # old distribute API - setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools')) + setuptools_dist = ws.find( + pkg_resources.Requirement.parse('setuptools') + ) if setuptools_dist is None: log.warn('No setuptools distribution found') @@ -414,7 +445,7 @@ def _fake_setuptools(): res = _patch_egg_dir(setuptools_location) if not res: return - log.warn('Patched done.') + log.warn('Patching complete.') _relaunch() @@ -422,7 +453,9 @@ def _relaunch(): log.warn('Relaunching...') # we have to relaunch the process # pip marker to avoid a relaunch bug - if sys.argv[:3] == ['-c', 'install', '--single-version-externally-managed']: + _cmd1 = ['-c', 'install', '--single-version-externally-managed'] + _cmd2 = ['-c', 'install', '--record'] + if sys.argv[:3] == _cmd1 or sys.argv[:3] == _cmd2: sys.argv[0] = 'setup.py' args = [sys.executable] + sys.argv sys.exit(subprocess.call(args)) @@ -448,7 +481,7 @@ def _extractall(self, path=".", members=None): # Extract directories with a safe mode. directories.append(tarinfo) tarinfo = copy.copy(tarinfo) - tarinfo.mode = 448 # decimal for oct 0700 + tarinfo.mode = 448 # decimal for oct 0700 self.extract(tarinfo, path) # Reverse sort directories. @@ -475,11 +508,39 @@ def _extractall(self, path=".", members=None): self._dbg(1, "tarfile: %s" % e) -def main(argv, version=DEFAULT_VERSION): +def _build_install_args(options): + """ + Build the arguments to 'python setup.py install' on the distribute package + """ + install_args = [] + if options.user_install: + if sys.version_info < (2, 6): + log.warn("--user requires Python 2.6 or later") + raise SystemExit(1) + install_args.append('--user') + return install_args + +def _parse_args(): + """ + Parse the command line for options + """ + parser = optparse.OptionParser() + parser.add_option( + '--user', dest='user_install', action='store_true', default=False, + help='install in user site package (requires Python 2.6 or later)') + parser.add_option( + '--download-base', dest='download_base', metavar="URL", + default=DEFAULT_URL, + help='alternative URL from where to download the distribute package') + options, args = parser.parse_args() + # positional arguments are ignored + return options + +def main(version=DEFAULT_VERSION): """Install or upgrade setuptools and EasyInstall""" - tarball = download_setuptools() - _install(tarball) - + options = _parse_args() + tarball = download_setuptools(download_base=options.download_base) + return _install(tarball, _build_install_args(options)) if __name__ == '__main__': - main(sys.argv[1:]) + sys.exit(main()) diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO index cc28edb..905bd25 100644 --- a/pysam.egg-info/PKG-INFO +++ b/pysam.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 1.1 Name: pysam -Version: 0.7.2 +Version: 0.7.3 Summary: pysam Home-page: http://code.google.com/p/pysam/ Author: Andreas Heger @@ -11,8 +11,6 @@ Description: pysam ***** - For more information, see http://code.google.com/p/pysam. - Platform: ALL -Requires: cython (>=0.16) +Requires: cython (>=0.17) diff --git a/pysam.egg-info/SOURCES.txt b/pysam.egg-info/SOURCES.txt index b59e914..8a914d5 100644 --- a/pysam.egg-info/SOURCES.txt +++ b/pysam.egg-info/SOURCES.txt @@ -12,6 +12,7 @@ pysam/TabProxies.pxd pysam/TabProxies.pyx pysam/VCF.py pysam/__init__.py +pysam/alternatives.py pysam/csamtools.c pysam/csamtools.pxd pysam/csamtools.pyx @@ -108,16 +109,22 @@ samtools/win32/xcurses.h samtools/win32/zconf.h samtools/win32/zlib.h tabix/bam_endian.h +tabix/bedidx.c tabix/bedidx.c.pysam.c +tabix/bgzf.c tabix/bgzf.c.pysam.c tabix/bgzf.h +tabix/bgzip.c tabix/bgzip.c.pysam.c +tabix/index.c tabix/index.c.pysam.c tabix/khash.h +tabix/knetfile.c tabix/knetfile.c.pysam.c tabix/knetfile.h tabix/kseq.h tabix/ksort.h +tabix/kstring.c tabix/kstring.c.pysam.c tabix/kstring.h tabix/pysam.h @@ -141,6 +148,7 @@ tests/example.gtf.gz tests/example.gtf.gz.tbi tests/example.py tests/example.vcf40 +tests/example_btag.bam tests/example_btag.sam tests/example_empty_header.bam tests/example_unmapped_reads_no_sq.sam diff --git a/pysam.egg-info/requires.txt b/pysam.egg-info/requires.txt index 3c6d9e8..9410b7b 100644 --- a/pysam.egg-info/requires.txt +++ b/pysam.egg-info/requires.txt @@ -1 +1 @@ -cython>=0.16 \ No newline at end of file +cython>=0.17 \ No newline at end of file diff --git a/pysam.egg-info/top_level.txt b/pysam.egg-info/top_level.txt index b030ff1..23f03da 100644 --- a/pysam.egg-info/top_level.txt +++ b/pysam.egg-info/top_level.txt @@ -1,5 +1 @@ -pysam/Pileup pysam -pysam/__init__ -pysam/version -pysam/namedtuple diff --git a/pysam/__init__.py b/pysam/__init__.py index c3a1266..e1d87ee 100644 --- a/pysam/__init__.py +++ b/pysam/__init__.py @@ -125,11 +125,10 @@ __all__ = \ [ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\ ["Pileup" ] -from version import __version__, __samtools_version__ +from pysam.version import __version__, __samtools_version__ def get_include(): - base = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'include')) - return [os.path.join(base, 'samtools'), os.path.join(base, 'pysam')] + return [os.path.abspath(os.path.join(os.path.dirname(__file__), 'include'))] def get_defines(): return [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')] diff --git a/pysam/alternatives.py b/pysam/alternatives.py new file mode 100644 index 0000000..fd76802 --- /dev/null +++ b/pysam/alternatives.py @@ -0,0 +1,82 @@ +# This file contains an alternative implementation +# to call samtools functions. These are direct calls. +# Plus: less overhead +# Minus: more trouble in maintaining + +#in csamtools.pxd + # samtools toolkit functions + ctypedef int (*pysam_samtools_f)(int argc, char *argv[]) + + int bam_taf2baf(int argc, char *argv[]) + int bam_pileup(int argc, char *argv[]) + int bam_merge(int argc, char *argv[]) + int bam_index(int argc, char *argv[]) + int bam_sort(int argc, char *argv[]) + int bam_tview_main(int argc, char *argv[]) + int bam_mating(int argc, char *argv[]) + int bam_rmdup(int argc, char *argv[]) + int bam_rmdupse(int argc, char *argv[]) + int bam_flagstat(int argc, char *argv[]) + int bam_fillmd(int argc, char *argv[]) + int main_samview(int argc, char *argv[]) + int main_import(int argc, char *argv[]) + int faidx_main(int argc, char *argv[]) + int glf3_view_main(int argc, char *argv[]) + + +## Alternative code in csamtools.pyx +cdef class SamtoolsWrapper: + '''generic wrapper around samtools functions''' + cdef pysam_samtools_f f + + def __init__(self): self.f = NULL + + def call(self, *args ): + + if self.f == NULL: raise NotImplementedError("invalid call to base class" ) + + cdef char ** cargs + cdef int i, n, retval + n = len(args) + # allocate one more for first (dummy) argument (contains command) + cargs = calloc( n+1, sizeof( char *) ) + cargs[0] = "method" + for i from 0 <= i < n: + cargs[i+1] = args[i] + for i from 0 <= i < n+1: + print cargs[i] + retval = self.f(n+1, cargs) + free( cargs ) + return retval + +cdef class SamtoolsWrapperImport( SamtoolsWrapper ): + def __init__(self): self.f = main_import +cdef class SamtoolsWrapperPileup( SamtoolsWrapper ): + def __init__(self): self.f = bam_pileup +cdef class SamtoolsWrapperMerge( SamtoolsWrapper ): + def __init__(self): self.f = bam_merge +cdef class SamtoolsWrapperSort( SamtoolsWrapper ): + def __init__(self): self.f = bam_sort +cdef class SamtoolsWrapperIndex( SamtoolsWrapper ): + def __init__(self): self.f = bam_index +cdef class SamtoolsWrapperFaidx( SamtoolsWrapper ): + def __init__(self): self.f = faidx_main +cdef class SamtoolsWrapperFixMate( SamtoolsWrapper ): + def __init__(self): self.f = bam_mating +cdef class SamtoolsWrapperRmDup( SamtoolsWrapper ): + def __init__(self): self.f = bam_rmdup +cdef class SamtoolsWrapperRmDupSe( SamtoolsWrapper ): + def __init__(self): self.f = bam_rmdupse +cdef class SamtoolsWrapperGlf3Viwen( SamtoolsWrapper ): + def __init__(self): self.f = glf3_view_main +cdef class SamtoolsWrapperFlagStat( SamtoolsWrapper ): + def __init__(self): self.f = bam_flagstat +cdef class SamtoolsWrapperFillMd( SamtoolsWrapper ): + def __init__(self): self.f = bam_fillmd +cdef class SamtoolsWrapperCalMd( SamtoolsWrapper ): + def __init__(self): self.f = bam_fillmd + +automatic creation of these functions does not work +due to pyrex/cython + +def sort( *args, **kwargs ): return SamtoolsWrapperSort().call(*args, **kwargs) diff --git a/pysam/ctabix.c b/pysam/ctabix.c index 8ed84fc..2a1ce55 100644 --- a/pysam/ctabix.c +++ b/pysam/ctabix.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.16 on Fri Nov 30 11:02:40 2012 */ +/* Generated by Cython 0.17.4 on Wed Jan 23 22:59:29 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -11,7 +11,6 @@ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif - #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall @@ -23,22 +22,18 @@ #define __fastcall #endif #endif - #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif - #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif - #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif - #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 @@ -46,28 +41,28 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif - -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyCFunction_Call PyObject_Call -#else - #define __Pyx_PyCFunction_Call PyCFunction_Call -#endif - #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" + #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) - #define PyNumber_Index(o) PyNumber_Int(o) - #define PyIndex_Check(o) PyNumber_Check(o) + #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ + (PyErr_Format(PyExc_TypeError, \ + "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ + (PyObject*)0)) + #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ + !PyComplex_Check(o)) + #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" + #define CYTHON_FORMAT_SSIZE_T "z" + #define __Pyx_PyIndex_Check PyIndex_Check #endif - #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) @@ -75,7 +70,6 @@ #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) - typedef struct { void *buf; PyObject *obj; @@ -89,7 +83,6 @@ Py_ssize_t *suboffsets; void *internal; } Py_buffer; - #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 @@ -101,11 +94,9 @@ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) - typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif - #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ @@ -115,31 +106,30 @@ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif - #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif - #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif - #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif - - -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH) +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #endif - #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject @@ -147,7 +137,6 @@ #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif - #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type @@ -166,7 +155,6 @@ #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif - #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) @@ -174,9 +162,7 @@ #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif - #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) - #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type @@ -193,11 +179,9 @@ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif - #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif - #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong @@ -206,7 +190,6 @@ #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif - #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) @@ -225,11 +208,9 @@ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif - #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif - #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) @@ -239,7 +220,6 @@ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif - #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) @@ -248,6 +228,7 @@ #define __Pyx_DOCSTR(n) (n) #endif + #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) @@ -268,8 +249,8 @@ #define _USE_MATH_DEFINES #endif #include -#define __PYX_HAVE__ctabix -#define __PYX_HAVE_API__ctabix +#define __PYX_HAVE__pysam__ctabix +#define __PYX_HAVE_API__pysam__ctabix #include "string.h" #include "stdlib.h" #include "stdio.h" @@ -336,7 +317,11 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); +#if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ @@ -366,51 +351,28 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { "ctabix.pyx", "TabProxies.pxd", + "type.pxd", "bool.pxd", "complex.pxd", }; /*--- Type declarations ---*/ -struct __pyx_obj_6ctabix_Parser; -struct __pyx_obj_6ctabix_asVCF; -struct __pyx_obj_10TabProxies_TupleProxy; -struct __pyx_obj_10TabProxies_NamedTupleProxy; -struct __pyx_obj_10TabProxies_BedProxy; -struct __pyx_obj_6ctabix_tabix_copy_iterator; -struct __pyx_obj_10TabProxies_VCFProxy; -struct __pyx_obj_10TabProxies_GTFProxy; -struct __pyx_obj_6ctabix_TabixIterator; -struct __pyx_obj_6ctabix_TabixIteratorParsed; -struct __pyx_obj_6ctabix_TabixHeaderIterator; -struct __pyx_obj_6ctabix_Tabixfile; -struct __pyx_obj_6ctabix_asGTF; -struct __pyx_obj_6ctabix_asBed; -struct __pyx_obj_6ctabix_tabix_inplace_iterator; -struct __pyx_obj_6ctabix_asTuple; - -/* "ctabix.pxd":190 - * cdef tabix_t * tabixfile - * - * cdef class Parser: # <<<<<<<<<<<<<< - * pass - * - */ -struct __pyx_obj_6ctabix_Parser { - PyObject_HEAD -}; - - -/* "ctabix.pxd":202 - * pass - * - * cdef class asVCF(Parser): # <<<<<<<<<<<<<< - * pass - * - */ -struct __pyx_obj_6ctabix_asVCF { - struct __pyx_obj_6ctabix_Parser __pyx_base; -}; - +struct __pyx_obj_5pysam_10TabProxies_TupleProxy; +struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy; +struct __pyx_obj_5pysam_10TabProxies_BedProxy; +struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator; +struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed; +struct __pyx_obj_5pysam_6ctabix_TabixIterator; +struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator; +struct __pyx_obj_5pysam_6ctabix_Parser; +struct __pyx_obj_5pysam_6ctabix_asTuple; +struct __pyx_obj_5pysam_6ctabix_asVCF; +struct __pyx_obj_5pysam_6ctabix_Tabixfile; +struct __pyx_obj_5pysam_6ctabix_asBed; +struct __pyx_obj_5pysam_6ctabix_asGTF; +struct __pyx_obj_5pysam_10TabProxies_VCFProxy; +struct __pyx_obj_5pysam_10TabProxies_GTFProxy; +struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator; /* "TabProxies.pxd":41 * ctypedef int uint64_t @@ -419,9 +381,9 @@ struct __pyx_obj_6ctabix_asVCF { * * cdef: */ -struct __pyx_obj_10TabProxies_TupleProxy { +struct __pyx_obj_5pysam_10TabProxies_TupleProxy { PyObject_HEAD - struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab; + struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab; char *data; char **fields; int nfields; @@ -439,8 +401,8 @@ struct __pyx_obj_10TabProxies_TupleProxy { * pass * */ -struct __pyx_obj_10TabProxies_NamedTupleProxy { - struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; +struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy { + struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; }; @@ -451,8 +413,8 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy { * * cdef: */ -struct __pyx_obj_10TabProxies_BedProxy { - struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base; +struct __pyx_obj_5pysam_10TabProxies_BedProxy { + struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t start; uint32_t end; @@ -460,100 +422,110 @@ struct __pyx_obj_10TabProxies_BedProxy { }; -/* "ctabix.pxd":218 - * cdef __cnext__(self) +/* "pysam/ctabix.pxd":186 + * cdef tabix_t * tabixfile * - * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef Parser parser + * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile */ -struct __pyx_obj_6ctabix_tabix_copy_iterator { +struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator { PyObject_HEAD - struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab; - FILE *infile; - struct __pyx_obj_6ctabix_Parser *parser; -}; - - -/* "TabProxies.pxd":83 - * cdef update( self, char * buffer, size_t nbytes ) - * - * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< - * - * cdef: - */ -struct __pyx_obj_10TabProxies_VCFProxy { - struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base; - char *contig; - uint32_t pos; + ti_iter_t iterator; + tabix_t *tabixfile; }; -/* "TabProxies.pxd":60 - * cdef update( self, char * buffer, size_t nbytes ) - * - * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< +/* "pysam/ctabix.pxd":205 + * pass * - * cdef: + * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile */ -struct __pyx_obj_10TabProxies_GTFProxy { - struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; - char *_attributes; - int hasOwnAttributes; +struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed { + PyObject_HEAD + ti_iter_t iterator; + tabix_t *tabixfile; + struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; -/* "ctabix.pxd":182 +/* "pysam/ctabix.pxd":182 * cdef char * _filename * * cdef class TabixIterator: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ -struct __pyx_obj_6ctabix_TabixIterator { +struct __pyx_obj_5pysam_6ctabix_TabixIterator { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; }; -/* "ctabix.pxd":205 - * pass +/* "pysam/ctabix.pxd":210 + * cdef Parser parser * - * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< - * cdef ti_iter_t iterator - * cdef tabix_t * tabixfile + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef char * buffer */ -struct __pyx_obj_6ctabix_TabixIteratorParsed { +struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator { PyObject_HEAD - ti_iter_t iterator; - tabix_t *tabixfile; - struct __pyx_obj_6ctabix_Parser *parser; + struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab; + FILE *infile; + char *buffer; + size_t size; + struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; -/* "ctabix.pxd":186 +/* "pysam/ctabix.pxd":190 * cdef tabix_t * tabixfile * - * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< - * cdef ti_iter_t iterator - * cdef tabix_t * tabixfile + * cdef class Parser: # <<<<<<<<<<<<<< + * pass + * */ -struct __pyx_obj_6ctabix_TabixHeaderIterator { +struct __pyx_obj_5pysam_6ctabix_Parser { PyObject_HEAD - ti_iter_t iterator; - tabix_t *tabixfile; }; -/* "ctabix.pxd":172 +/* "pysam/ctabix.pxd":193 + * pass + * + * cdef class asTuple(Parser): # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_5pysam_6ctabix_asTuple { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; +}; + + +/* "pysam/ctabix.pxd":202 + * pass + * + * cdef class asVCF(Parser): # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_5pysam_6ctabix_asVCF { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; +}; + + +/* "pysam/ctabix.pxd":172 * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) * * cdef class Tabixfile: # <<<<<<<<<<<<<< * * # pointer to tabixfile */ -struct __pyx_obj_6ctabix_Tabixfile { +struct __pyx_obj_5pysam_6ctabix_Tabixfile { PyObject_HEAD tabix_t *tabixfile; int isremote; @@ -561,72 +533,72 @@ struct __pyx_obj_6ctabix_Tabixfile { }; -/* "ctabix.pxd":196 +/* "pysam/ctabix.pxd":199 * pass * - * cdef class asGTF(Parser): # <<<<<<<<<<<<<< + * cdef class asBed(Parser): # <<<<<<<<<<<<<< * pass * */ -struct __pyx_obj_6ctabix_asGTF { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_5pysam_6ctabix_asBed { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; -/* "ctabix.pxd":199 +/* "pysam/ctabix.pxd":196 * pass * - * cdef class asBed(Parser): # <<<<<<<<<<<<<< + * cdef class asGTF(Parser): # <<<<<<<<<<<<<< * pass * */ -struct __pyx_obj_6ctabix_asBed { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_5pysam_6ctabix_asGTF { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; -/* "ctabix.pxd":210 - * cdef Parser parser +/* "TabProxies.pxd":83 + * cdef update( self, char * buffer, size_t nbytes ) * - * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef char * buffer + * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< + * + * cdef: */ -struct __pyx_obj_6ctabix_tabix_inplace_iterator { - PyObject_HEAD - struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab; - FILE *infile; - char *buffer; - size_t size; - struct __pyx_obj_6ctabix_Parser *parser; +struct __pyx_obj_5pysam_10TabProxies_VCFProxy { + struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; + char *contig; + uint32_t pos; }; -/* "ctabix.pxd":193 - * pass +/* "TabProxies.pxd":60 + * cdef update( self, char * buffer, size_t nbytes ) * - * cdef class asTuple(Parser): # <<<<<<<<<<<<<< - * pass + * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * + * cdef: */ -struct __pyx_obj_6ctabix_asTuple { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_5pysam_10TabProxies_GTFProxy { + struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; + char *_attributes; + int hasOwnAttributes; }; - -/* "ctabix.pyx":771 - * return self.__cnext__() +/* "pysam/ctabix.pxd":218 + * cdef __cnext__(self) * * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< - * '''iterate over ``infile``. - * + * cdef FILE * infile + * cdef Parser parser */ - -struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator { - PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *); +struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator { + PyObject_HEAD + struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab; + FILE *infile; + struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; -static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator; + /* "TabProxies.pxd":41 @@ -637,14 +609,14 @@ static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabi * cdef: */ -struct __pyx_vtabstruct_10TabProxies_TupleProxy { - int (*getMaxFields)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t); - PyObject *(*take)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); - PyObject *(*present)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); - PyObject *(*copy)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); - PyObject *(*update)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); +struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy { + int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t); + PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); + PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); + PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); + PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); }; -static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy; /* "TabProxies.pxd":69 @@ -655,10 +627,10 @@ static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxi * */ -struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy { - struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base; +struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy; /* "TabProxies.pxd":83 @@ -669,10 +641,24 @@ static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10Tab * cdef: */ -struct __pyx_vtabstruct_10TabProxies_VCFProxy { - struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; +struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy; + + +/* "pysam/ctabix.pyx":709 + * ## Iterators for parsing through unindexed files. + * ######################################################### + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * '''iterate over ``infile``. + * + */ + +struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *); +}; +static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator; /* "TabProxies.pxd":60 @@ -683,39 +669,39 @@ static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies * cdef: */ -struct __pyx_vtabstruct_10TabProxies_GTFProxy { - struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base; - char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *); +struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; + char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *); }; -static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy; -/* "TabProxies.pxd":72 - * pass +/* "pysam/ctabix.pyx":771 + * return self.__cnext__() * - * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< + * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< + * '''iterate over ``infile``. * - * cdef: */ -struct __pyx_vtabstruct_10TabProxies_BedProxy { - struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; +struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *); }; -static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy; +static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator; -/* "ctabix.pyx":709 - * ## Iterators for parsing through unindexed files. - * ######################################################### - * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< - * '''iterate over ``infile``. +/* "TabProxies.pxd":72 + * pass + * + * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * + * cdef: */ -struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator { - PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *); +struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator; +static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy; #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -772,6 +758,11 @@ static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ct static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ @@ -799,42 +790,47 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j __Pyx_GetItemInt_List_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { - if (likely(o != Py_None)) { - if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, i); - Py_INCREF(r); - return r; - } - else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) { - PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i); - Py_INCREF(r); - return r; - } +#if CYTHON_COMPILING_IN_CPYTHON + if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i); + Py_INCREF(r); + return r; } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif } #define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_Tuple_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { - if (likely(o != Py_None)) { - if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, i); - Py_INCREF(r); - return r; - } - else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) { - PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i); - Py_INCREF(r); - return r; - } +#if CYTHON_COMPILING_IN_CPYTHON + if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i); + Py_INCREF(r); + return r; } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif } #define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) { +#if CYTHON_COMPILING_IN_CPYTHON if (PyList_CheckExact(o)) { Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { @@ -850,34 +846,39 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) Py_INCREF(r); return r; } - } - else if (likely(i >= 0)) { + } else { /* inlined PySequence_GetItem() */ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; if (likely(m && m->sq_item)) { + if (unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (unlikely(l < 0)) return NULL; + i += l; + } return m->sq_item(o, i); } } +#else + if (PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); +static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); /*proto*/ -static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void); - #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; - if (unlikely(d == Py_None)) { - __Pyx_RaiseNoneIndexingError(); - return NULL; - } value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (!PyErr_Occurred()) @@ -945,16 +946,6 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, PyObject *tuple); static int __Pyx_CyFunction_init(void); -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ - -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ - -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *); static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); @@ -1001,10 +992,10 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ #endif #endif -static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ - static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ + static void* __Pyx_GetVtable(PyObject *dict); /*proto*/ typedef struct { @@ -1027,12 +1018,14 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ -/* Module declarations from 'TabProxies' */ -static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0; +/* Module declarations from 'pysam' */ + +/* Module declarations from 'pysam.TabProxies' */ +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0; /* Module declarations from 'cpython.version' */ @@ -1058,7 +1051,10 @@ static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0; /* Module declarations from 'cpython.iterator' */ +/* Module declarations from '__builtin__' */ + /* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; /* Module declarations from 'cpython.number' */ @@ -1112,26 +1108,26 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; /* Module declarations from 'cpython' */ -/* Module declarations from 'ctabix' */ -static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0; -static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0; -static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 0; -static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asTuple = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asGTF = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asBed = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0; -static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0; -static PyTypeObject *__pyx_ptype_6ctabix_tabix_inplace_iterator = 0; -static PyTypeObject *__pyx_ptype_6ctabix_tabix_copy_iterator = 0; -static PyObject *__pyx_v_6ctabix__FILENAME_ENCODING = 0; -static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *); /*proto*/ -static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *); /*proto*/ -static PyObject *__pyx_f_6ctabix__charptr_to_str(char *); /*proto*/ -#define __Pyx_MODULE_NAME "ctabix" -int __pyx_module_is_main_ctabix = 0; - -/* Implementation of 'ctabix' */ +/* Module declarations from 'pysam.ctabix' */ +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Parser = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = 0; +static PyObject *__pyx_v_5pysam_6ctabix__FILENAME_ENCODING = 0; +static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *); /*proto*/ +static PyObject *__pyx_f_5pysam_6ctabix__force_bytes(PyObject *); /*proto*/ +static PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *); /*proto*/ +#define __Pyx_MODULE_NAME "pysam.ctabix" +int __pyx_module_is_main_pysam__ctabix = 0; + +/* Implementation of 'pysam.ctabix' */ static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_builtin_IOError; @@ -1141,46 +1137,46 @@ static PyObject *__pyx_builtin_OSError; static PyObject *__pyx_builtin_ord; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_MemoryError; -static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_10close(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */ -static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */ -static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end); /* proto */ -static PyObject *__pyx_pf_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */ -static void __pyx_pf_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */ -static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile); /* proto */ -static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ -static void __pyx_pf_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ -static PyObject *__pyx_pf_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ -static PyObject *__pyx_pf_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ -static PyObject *__pyx_pf_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ -static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser); /* proto */ -static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ -static void __pyx_pf_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */ -static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */ -static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size); /* proto */ -static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ -static void __pyx_pf_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ -static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser); /* proto */ -static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ +static int __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_10close(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ +static void __pyx_pf_5pysam_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ +static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ +static void __pyx_pf_5pysam_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ +static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ +static void __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ +static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ +static void __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */ +static int __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ +static void __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */ +static int __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ static char __pyx_k_1[] = "Argument must be string or unicode."; static char __pyx_k_3[] = "Argument must be string, bytes or unicode."; static char __pyx_k_5[] = "invalid file opening mode `%s`"; @@ -1218,8 +1214,9 @@ static char __pyx_k_60[] = "the file header.\n \n .. note::\n static char __pyx_k_61[] = "chromosome names"; static char __pyx_k_62[] = "getfilesystemencoding"; static char __pyx_k_65[] = "/ifs/devel/pysam/pysam/ctabix.pyx"; -static char __pyx_k_76[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n "; -static char __pyx_k_79[] = "tabix_inplace_iterator"; +static char __pyx_k_66[] = "pysam.ctabix"; +static char __pyx_k_77[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n "; +static char __pyx_k_80[] = "tabix_inplace_iterator"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__r[] = "r"; @@ -1259,7 +1256,6 @@ static char __pyx_k__types[] = "types"; static char __pyx_k__Parser[] = "Parser"; static char __pyx_k__buffer[] = "buffer"; static char __pyx_k__closed[] = "closed"; -static char __pyx_k__ctabix[] = "ctabix"; static char __pyx_k__ctypes[] = "ctypes"; static char __pyx_k__decode[] = "decode"; static char __pyx_k__encode[] = "encode"; @@ -1350,9 +1346,10 @@ static PyObject *__pyx_n_s_58; static PyObject *__pyx_kp_s_6; static PyObject *__pyx_n_s_62; static PyObject *__pyx_kp_s_65; +static PyObject *__pyx_n_s_66; static PyObject *__pyx_kp_s_7; -static PyObject *__pyx_kp_s_76; -static PyObject *__pyx_n_s_79; +static PyObject *__pyx_kp_s_77; +static PyObject *__pyx_n_s_80; static PyObject *__pyx_kp_s_9; static PyObject *__pyx_n_s__IOError; static PyObject *__pyx_n_s__KeyError; @@ -1391,7 +1388,6 @@ static PyObject *__pyx_n_s__closed; static PyObject *__pyx_n_s__conf; static PyObject *__pyx_n_s__conf_data; static PyObject *__pyx_n_s__cpy; -static PyObject *__pyx_n_s__ctabix; static PyObject *__pyx_n_s__ctypes; static PyObject *__pyx_n_s__decode; static PyObject *__pyx_n_s__encode; @@ -1491,21 +1487,21 @@ static PyObject *__pyx_k_tuple_55; static PyObject *__pyx_k_tuple_56; static PyObject *__pyx_k_tuple_57; static PyObject *__pyx_k_tuple_63; -static PyObject *__pyx_k_tuple_66; -static PyObject *__pyx_k_tuple_68; -static PyObject *__pyx_k_tuple_70; -static PyObject *__pyx_k_tuple_72; -static PyObject *__pyx_k_tuple_74; -static PyObject *__pyx_k_tuple_77; +static PyObject *__pyx_k_tuple_67; +static PyObject *__pyx_k_tuple_69; +static PyObject *__pyx_k_tuple_71; +static PyObject *__pyx_k_tuple_73; +static PyObject *__pyx_k_tuple_75; +static PyObject *__pyx_k_tuple_78; static PyObject *__pyx_k_codeobj_64; -static PyObject *__pyx_k_codeobj_67; -static PyObject *__pyx_k_codeobj_69; -static PyObject *__pyx_k_codeobj_71; -static PyObject *__pyx_k_codeobj_73; -static PyObject *__pyx_k_codeobj_75; -static PyObject *__pyx_k_codeobj_78; - -/* "ctabix.pyx":19 +static PyObject *__pyx_k_codeobj_68; +static PyObject *__pyx_k_codeobj_70; +static PyObject *__pyx_k_codeobj_72; +static PyObject *__pyx_k_codeobj_74; +static PyObject *__pyx_k_codeobj_76; +static PyObject *__pyx_k_codeobj_79; + +/* "pysam/ctabix.pyx":19 * from cpython.version cimport PY_MAJOR_VERSION * * cdef from_string_and_size(char* s, size_t length): # <<<<<<<<<<<<<< @@ -1513,7 +1509,7 @@ static PyObject *__pyx_k_codeobj_78; * return s[:length] */ -static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { +static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -1523,7 +1519,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("from_string_and_size", 0); - /* "ctabix.pyx":20 + /* "pysam/ctabix.pyx":20 * * cdef from_string_and_size(char* s, size_t length): * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<< @@ -1533,7 +1529,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ __pyx_t_1 = (PY_MAJOR_VERSION < 3); if (__pyx_t_1) { - /* "ctabix.pyx":21 + /* "pysam/ctabix.pyx":21 * cdef from_string_and_size(char* s, size_t length): * if PY_MAJOR_VERSION < 3: * return s[:length] # <<<<<<<<<<<<<< @@ -1541,7 +1537,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ * return s[:length].decode("ascii") */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_s + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyBytes_FromStringAndSize(((const char*)__pyx_v_s) + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; @@ -1550,7 +1546,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ } /*else*/ { - /* "ctabix.pyx":23 + /* "pysam/ctabix.pyx":23 * return s[:length] * else: * return s[:length].decode("ascii") # <<<<<<<<<<<<<< @@ -1558,7 +1554,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ * # filename encoding (copied from lxml.etree.pyx) */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; @@ -1570,7 +1566,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -1578,7 +1574,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ return __pyx_r; } -/* "ctabix.pyx":36 +/* "pysam/ctabix.pyx":36 * #_C_FILENAME_ENCODING = _FILENAME_ENCODING * * cdef bytes _my_encodeFilename(object filename): # <<<<<<<<<<<<<< @@ -1586,7 +1582,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __ * """ */ -static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) { +static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -1598,7 +1594,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_my_encodeFilename", 0); - /* "ctabix.pyx":39 + /* "pysam/ctabix.pyx":39 * u"""Make sure a filename is 8-bit encoded (or None). * """ * if filename is None: # <<<<<<<<<<<<<< @@ -1608,7 +1604,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) __pyx_t_1 = (__pyx_v_filename == Py_None); if (__pyx_t_1) { - /* "ctabix.pyx":40 + /* "pysam/ctabix.pyx":40 * """ * if filename is None: * return None # <<<<<<<<<<<<<< @@ -1622,7 +1618,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) goto __pyx_L3; } - /* "ctabix.pyx":41 + /* "pysam/ctabix.pyx":41 * if filename is None: * return None * elif PyBytes_Check(filename): # <<<<<<<<<<<<<< @@ -1632,7 +1628,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) __pyx_t_1 = PyBytes_Check(__pyx_v_filename); if (__pyx_t_1) { - /* "ctabix.pyx":42 + /* "pysam/ctabix.pyx":42 * return None * elif PyBytes_Check(filename): * return filename # <<<<<<<<<<<<<< @@ -1647,7 +1643,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) goto __pyx_L3; } - /* "ctabix.pyx":43 + /* "pysam/ctabix.pyx":43 * elif PyBytes_Check(filename): * return filename * elif PyUnicode_Check(filename): # <<<<<<<<<<<<<< @@ -1657,7 +1653,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) __pyx_t_1 = PyUnicode_Check(__pyx_v_filename); if (__pyx_t_1) { - /* "ctabix.pyx":44 + /* "pysam/ctabix.pyx":44 * return filename * elif PyUnicode_Check(filename): * return filename.encode(_FILENAME_ENCODING) # <<<<<<<<<<<<<< @@ -1669,9 +1665,9 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __Pyx_INCREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); - PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); - __Pyx_GIVEREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); + __Pyx_INCREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); + PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); + __Pyx_GIVEREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -1684,7 +1680,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) } /*else*/ { - /* "ctabix.pyx":46 + /* "pysam/ctabix.pyx":46 * return filename.encode(_FILENAME_ENCODING) * else: * raise TypeError, u"Argument must be string or unicode." # <<<<<<<<<<<<<< @@ -1702,7 +1698,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); - __Pyx_AddTraceback("ctabix._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -1710,7 +1706,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) return __pyx_r; } -/* "ctabix.pyx":48 +/* "pysam/ctabix.pyx":48 * raise TypeError, u"Argument must be string or unicode." * * cdef bytes _force_bytes(object s): # <<<<<<<<<<<<<< @@ -1718,7 +1714,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) * """ */ -static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { +static PyObject *__pyx_f_5pysam_6ctabix__force_bytes(PyObject *__pyx_v_s) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -1729,7 +1725,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_force_bytes", 0); - /* "ctabix.pyx":51 + /* "pysam/ctabix.pyx":51 * u"""convert string or unicode object to bytes, assuming ascii encoding. * """ * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<< @@ -1739,7 +1735,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { __pyx_t_1 = (PY_MAJOR_VERSION < 3); if (__pyx_t_1) { - /* "ctabix.pyx":52 + /* "pysam/ctabix.pyx":52 * """ * if PY_MAJOR_VERSION < 3: * return s # <<<<<<<<<<<<<< @@ -1754,7 +1750,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { goto __pyx_L3; } - /* "ctabix.pyx":53 + /* "pysam/ctabix.pyx":53 * if PY_MAJOR_VERSION < 3: * return s * elif s is None: # <<<<<<<<<<<<<< @@ -1764,7 +1760,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { __pyx_t_1 = (__pyx_v_s == Py_None); if (__pyx_t_1) { - /* "ctabix.pyx":54 + /* "pysam/ctabix.pyx":54 * return s * elif s is None: * return None # <<<<<<<<<<<<<< @@ -1778,7 +1774,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { goto __pyx_L3; } - /* "ctabix.pyx":55 + /* "pysam/ctabix.pyx":55 * elif s is None: * return None * elif PyBytes_Check(s): # <<<<<<<<<<<<<< @@ -1788,7 +1784,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { __pyx_t_1 = PyBytes_Check(__pyx_v_s); if (__pyx_t_1) { - /* "ctabix.pyx":56 + /* "pysam/ctabix.pyx":56 * return None * elif PyBytes_Check(s): * return s # <<<<<<<<<<<<<< @@ -1803,7 +1799,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { goto __pyx_L3; } - /* "ctabix.pyx":57 + /* "pysam/ctabix.pyx":57 * elif PyBytes_Check(s): * return s * elif PyUnicode_Check(s): # <<<<<<<<<<<<<< @@ -1813,7 +1809,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { __pyx_t_1 = PyUnicode_Check(__pyx_v_s); if (__pyx_t_1) { - /* "ctabix.pyx":58 + /* "pysam/ctabix.pyx":58 * return s * elif PyUnicode_Check(s): * return s.encode('ascii') # <<<<<<<<<<<<<< @@ -1834,7 +1830,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { } /*else*/ { - /* "ctabix.pyx":60 + /* "pysam/ctabix.pyx":60 * return s.encode('ascii') * else: * raise TypeError, u"Argument must be string, bytes or unicode." # <<<<<<<<<<<<<< @@ -1851,7 +1847,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("ctabix._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -1859,7 +1855,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { return __pyx_r; } -/* "ctabix.pyx":62 +/* "pysam/ctabix.pyx":62 * raise TypeError, u"Argument must be string, bytes or unicode." * * cdef inline bytes _force_cmdline_bytes(object s): # <<<<<<<<<<<<<< @@ -1867,7 +1863,7 @@ static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *__pyx_v_s) { * */ -static CYTHON_INLINE PyObject *__pyx_f_6ctabix__force_cmdline_bytes(PyObject *__pyx_v_s) { +static CYTHON_INLINE PyObject *__pyx_f_5pysam_6ctabix__force_cmdline_bytes(PyObject *__pyx_v_s) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -1876,7 +1872,7 @@ static CYTHON_INLINE PyObject *__pyx_f_6ctabix__force_cmdline_bytes(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_force_cmdline_bytes", 0); - /* "ctabix.pyx":63 + /* "pysam/ctabix.pyx":63 * * cdef inline bytes _force_cmdline_bytes(object s): * return _force_bytes(s) # <<<<<<<<<<<<<< @@ -1884,7 +1880,7 @@ static CYTHON_INLINE PyObject *__pyx_f_6ctabix__force_cmdline_bytes(PyObject *__ * cdef _charptr_to_str(char* s): */ __Pyx_XDECREF(((PyObject *)__pyx_r)); - __pyx_t_1 = ((PyObject *)__pyx_f_6ctabix__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_6ctabix__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; @@ -1894,7 +1890,7 @@ static CYTHON_INLINE PyObject *__pyx_f_6ctabix__force_cmdline_bytes(PyObject *__ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -1902,7 +1898,7 @@ static CYTHON_INLINE PyObject *__pyx_f_6ctabix__force_cmdline_bytes(PyObject *__ return __pyx_r; } -/* "ctabix.pyx":65 +/* "pysam/ctabix.pyx":65 * return _force_bytes(s) * * cdef _charptr_to_str(char* s): # <<<<<<<<<<<<<< @@ -1910,7 +1906,7 @@ static CYTHON_INLINE PyObject *__pyx_f_6ctabix__force_cmdline_bytes(PyObject *__ * return s */ -static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { +static PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *__pyx_v_s) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -1920,7 +1916,7 @@ static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_charptr_to_str", 0); - /* "ctabix.pyx":66 + /* "pysam/ctabix.pyx":66 * * cdef _charptr_to_str(char* s): * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<< @@ -1930,7 +1926,7 @@ static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { __pyx_t_1 = (PY_MAJOR_VERSION < 3); if (__pyx_t_1) { - /* "ctabix.pyx":67 + /* "pysam/ctabix.pyx":67 * cdef _charptr_to_str(char* s): * if PY_MAJOR_VERSION < 3: * return s # <<<<<<<<<<<<<< @@ -1947,7 +1943,7 @@ static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { } /*else*/ { - /* "ctabix.pyx":69 + /* "pysam/ctabix.pyx":69 * return s * else: * return s.decode("ascii") # <<<<<<<<<<<<<< @@ -1955,7 +1951,7 @@ static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { * cdef _force_str(object s): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, strlen(__pyx_v_s), NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, strlen(__pyx_v_s), NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; @@ -1967,7 +1963,7 @@ static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -1975,7 +1971,7 @@ static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { return __pyx_r; } -/* "ctabix.pyx":71 +/* "pysam/ctabix.pyx":71 * return s.decode("ascii") * * cdef _force_str(object s): # <<<<<<<<<<<<<< @@ -1983,7 +1979,7 @@ static PyObject *__pyx_f_6ctabix__charptr_to_str(char *__pyx_v_s) { * if s is None: */ -static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { +static PyObject *__pyx_f_5pysam_6ctabix__force_str(PyObject *__pyx_v_s) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -1994,7 +1990,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_force_str", 0); - /* "ctabix.pyx":73 + /* "pysam/ctabix.pyx":73 * cdef _force_str(object s): * """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)""" * if s is None: # <<<<<<<<<<<<<< @@ -2004,7 +2000,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { __pyx_t_1 = (__pyx_v_s == Py_None); if (__pyx_t_1) { - /* "ctabix.pyx":74 + /* "pysam/ctabix.pyx":74 * """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)""" * if s is None: * return None # <<<<<<<<<<<<<< @@ -2019,7 +2015,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { } __pyx_L3:; - /* "ctabix.pyx":75 + /* "pysam/ctabix.pyx":75 * if s is None: * return None * if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<< @@ -2029,7 +2025,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { __pyx_t_1 = (PY_MAJOR_VERSION < 3); if (__pyx_t_1) { - /* "ctabix.pyx":76 + /* "pysam/ctabix.pyx":76 * return None * if PY_MAJOR_VERSION < 3: * return s # <<<<<<<<<<<<<< @@ -2043,7 +2039,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { goto __pyx_L4; } - /* "ctabix.pyx":77 + /* "pysam/ctabix.pyx":77 * if PY_MAJOR_VERSION < 3: * return s * elif PyBytes_Check(s): # <<<<<<<<<<<<<< @@ -2053,7 +2049,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { __pyx_t_1 = PyBytes_Check(__pyx_v_s); if (__pyx_t_1) { - /* "ctabix.pyx":78 + /* "pysam/ctabix.pyx":78 * return s * elif PyBytes_Check(s): * return s.decode('ascii') # <<<<<<<<<<<<<< @@ -2073,7 +2069,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { } /*else*/ { - /* "ctabix.pyx":81 + /* "pysam/ctabix.pyx":81 * else: * # assume unicode * return s # <<<<<<<<<<<<<< @@ -2092,7 +2088,7 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("ctabix._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -2101,13 +2097,12 @@ static PyObject *__pyx_f_6ctabix__force_str(PyObject *__pyx_v_s) { } /* Python wrapper */ -static int __pyx_pw_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_filename = 0; PyObject *__pyx_v_mode = 0; PyObject *__pyx_v_args = 0; PyObject *__pyx_v_kwargs = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0}; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); @@ -2125,6 +2120,7 @@ static int __pyx_pw_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObje __pyx_v_args = __pyx_empty_tuple; __Pyx_INCREF(__pyx_empty_tuple); } { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0}; PyObject* values[2] = {0,0}; values[1] = ((PyObject *)__pyx_n_s__r); if (unlikely(__pyx_kwds)) { @@ -2139,8 +2135,7 @@ static int __pyx_pw_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObje kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (kw_args > 0) { @@ -2171,18 +2166,18 @@ static int __pyx_pw_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObje __pyx_L3_error:; __Pyx_DECREF(__pyx_v_args); __pyx_v_args = 0; __Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0; - __Pyx_AddTraceback("ctabix.Tabixfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_9Tabixfile___cinit__(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_args, __pyx_v_kwargs); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_args, __pyx_v_kwargs); __Pyx_XDECREF(__pyx_v_args); __Pyx_XDECREF(__pyx_v_kwargs); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":90 +/* "pysam/ctabix.pyx":90 * index (*filename* + ".tbi") will raise an exception. * ''' * def __cinit__(self, filename, mode = 'r', *args, **kwargs ): # <<<<<<<<<<<<<< @@ -2190,7 +2185,7 @@ static int __pyx_pw_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self, PyObje * self._open( filename, mode, *args, **kwargs ) */ -static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) { +static int __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) { int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -2202,7 +2197,7 @@ static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixf int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "ctabix.pyx":91 + /* "pysam/ctabix.pyx":91 * ''' * def __cinit__(self, filename, mode = 'r', *args, **kwargs ): * self.tabixfile = NULL # <<<<<<<<<<<<<< @@ -2211,7 +2206,7 @@ static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixf */ __pyx_v_self->tabixfile = NULL; - /* "ctabix.pyx":92 + /* "pysam/ctabix.pyx":92 * def __cinit__(self, filename, mode = 'r', *args, **kwargs ): * self.tabixfile = NULL * self._open( filename, mode, *args, **kwargs ) # <<<<<<<<<<<<<< @@ -2250,7 +2245,7 @@ static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixf __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); - __Pyx_AddTraceback("ctabix.Tabixfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -2258,18 +2253,18 @@ static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixf } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_6ctabix_9Tabixfile_2_isOpen[] = "Tabixfile._isOpen(self)\nreturn true if samfile has been opened."; -static PyObject *__pyx_pw_6ctabix_9Tabixfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_9Tabixfile_2_isOpen[] = "Tabixfile._isOpen(self)\nreturn true if samfile has been opened."; +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_2_isOpen(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_2_isOpen(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":94 +/* "pysam/ctabix.pyx":94 * self._open( filename, mode, *args, **kwargs ) * * def _isOpen( self ): # <<<<<<<<<<<<<< @@ -2277,7 +2272,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_3_isOpen(PyObject *__pyx_v_self, CY * return self.tabixfile != NULL */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -2286,7 +2281,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_6ctabix_T int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_isOpen", 0); - /* "ctabix.pyx":96 + /* "pysam/ctabix.pyx":96 * def _isOpen( self ): * '''return true if samfile has been opened.''' * return self.tabixfile != NULL # <<<<<<<<<<<<<< @@ -2304,7 +2299,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_6ctabix_T goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.Tabixfile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -2313,16 +2308,16 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_6ctabix_T } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_6ctabix_9Tabixfile_4_open[] = "Tabixfile._open(self, filename, mode='r')\nopen a :term:`tabix file` for reading.\n "; -static PyObject *__pyx_pw_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_9Tabixfile_4_open[] = "Tabixfile._open(self, filename, mode='r')\nopen a :term:`tabix file` for reading.\n "; +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_filename = 0; PyObject *__pyx_v_mode = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("_open (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0}; PyObject* values[2] = {0,0}; values[1] = ((PyObject *)__pyx_n_s__r); if (unlikely(__pyx_kwds)) { @@ -2337,8 +2332,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyOb kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (kw_args > 0) { @@ -2364,16 +2358,16 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyOb __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("_open", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.Tabixfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_4_open(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":98 +/* "pysam/ctabix.pyx":98 * return self.tabixfile != NULL * * def _open( self, # <<<<<<<<<<<<<< @@ -2381,14 +2375,14 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyOb * mode ='r', */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode) { PyObject *__pyx_v_filename_index = NULL; CYTHON_UNUSED PyObject *__pyx_v_bmode = 0; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; - int __pyx_t_2; - PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; PyObject *__pyx_t_4 = NULL; int __pyx_t_5; char *__pyx_t_6; @@ -2400,7 +2394,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab __Pyx_RefNannySetupContext("_open", 0); __Pyx_INCREF(__pyx_v_filename); - /* "ctabix.pyx":105 + /* "pysam/ctabix.pyx":105 * ''' * * assert mode in ( "r",), "invalid file opening mode `%s`" % mode # <<<<<<<<<<<<<< @@ -2410,9 +2404,11 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab #ifndef CYTHON_WITHOUT_ASSERTIONS __Pyx_INCREF(__pyx_v_mode); __pyx_t_1 = __pyx_v_mode; - __pyx_t_2 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - if (unlikely(!((int)__pyx_t_2))) { + if (unlikely(!((int)__pyx_t_3))) { __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_5), __pyx_v_mode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_1)); @@ -2421,26 +2417,26 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab } #endif - /* "ctabix.pyx":108 + /* "pysam/ctabix.pyx":108 * * # close a previously opened file * if self.tabixfile != NULL: self.close() # <<<<<<<<<<<<<< * self.tabixfile = NULL * */ - __pyx_t_2 = (__pyx_v_self->tabixfile != NULL); - if (__pyx_t_2) { + __pyx_t_3 = (__pyx_v_self->tabixfile != NULL); + if (__pyx_t_3) { __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L3; } __pyx_L3:; - /* "ctabix.pyx":109 + /* "pysam/ctabix.pyx":109 * # close a previously opened file * if self.tabixfile != NULL: self.close() * self.tabixfile = NULL # <<<<<<<<<<<<<< @@ -2449,105 +2445,105 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab */ __pyx_v_self->tabixfile = NULL; - /* "ctabix.pyx":111 + /* "pysam/ctabix.pyx":111 * self.tabixfile = NULL * * filename_index = filename + ".tbi" # <<<<<<<<<<<<<< * self.isremote = filename.startswith( "http:") or filename.startswith( "ftp:" ) * */ - __pyx_t_3 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_v_filename_index = __pyx_t_3; - __pyx_t_3 = 0; + __pyx_t_2 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_v_filename_index = __pyx_t_2; + __pyx_t_2 = 0; - /* "ctabix.pyx":112 + /* "pysam/ctabix.pyx":112 * * filename_index = filename + ".tbi" * self.isremote = filename.startswith( "http:") or filename.startswith( "ftp:" ) # <<<<<<<<<<<<<< * * # encode all the strings */ - __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (!__pyx_t_2) { + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!__pyx_t_3) { __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __pyx_t_4; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = __pyx_t_4; __pyx_t_4 = 0; } else { - __pyx_t_3 = __pyx_t_1; + __pyx_t_2 = __pyx_t_1; __pyx_t_1 = 0; } - __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_v_self->isremote = __pyx_t_5; - /* "ctabix.pyx":115 + /* "pysam/ctabix.pyx":115 * * # encode all the strings * filename = _my_encodeFilename(filename) # <<<<<<<<<<<<<< * filename_index = _my_encodeFilename(filename_index) * cdef bytes bmode = mode.encode('ascii') */ - __pyx_t_3 = ((PyObject *)__pyx_f_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_filename); - __pyx_v_filename = __pyx_t_3; - __pyx_t_3 = 0; + __pyx_v_filename = __pyx_t_2; + __pyx_t_2 = 0; - /* "ctabix.pyx":116 + /* "pysam/ctabix.pyx":116 * # encode all the strings * filename = _my_encodeFilename(filename) * filename_index = _my_encodeFilename(filename_index) # <<<<<<<<<<<<<< * cdef bytes bmode = mode.encode('ascii') * */ - __pyx_t_3 = ((PyObject *)__pyx_f_6ctabix__my_encodeFilename(__pyx_v_filename_index)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_6ctabix__my_encodeFilename(__pyx_v_filename_index)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_filename_index); - __pyx_v_filename_index = __pyx_t_3; - __pyx_t_3 = 0; + __pyx_v_filename_index = __pyx_t_2; + __pyx_t_2 = 0; - /* "ctabix.pyx":117 + /* "pysam/ctabix.pyx":117 * filename = _my_encodeFilename(filename) * filename_index = _my_encodeFilename(filename_index) * cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<< * * if self._filename != NULL: free(self._filename ) */ - __pyx_t_3 = PyObject_GetAttr(__pyx_v_mode, __pyx_n_s__encode); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_11), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_mode, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_11), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_bmode = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":119 + /* "pysam/ctabix.pyx":119 * cdef bytes bmode = mode.encode('ascii') * * if self._filename != NULL: free(self._filename ) # <<<<<<<<<<<<<< * * self._filename = strdup(filename) */ - __pyx_t_2 = (__pyx_v_self->_filename != NULL); - if (__pyx_t_2) { + __pyx_t_3 = (__pyx_v_self->_filename != NULL); + if (__pyx_t_3) { free(__pyx_v_self->_filename); goto __pyx_L4; } __pyx_L4:; - /* "ctabix.pyx":121 + /* "pysam/ctabix.pyx":121 * if self._filename != NULL: free(self._filename ) * * self._filename = strdup(filename) # <<<<<<<<<<<<<< @@ -2557,7 +2553,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab __pyx_t_6 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_self->_filename = strdup(__pyx_t_6); - /* "ctabix.pyx":123 + /* "pysam/ctabix.pyx":123 * self._filename = strdup(filename) * * if mode[0] == 'w': # <<<<<<<<<<<<<< @@ -2566,49 +2562,53 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab */ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__w), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - if (__pyx_t_2) { + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + if (__pyx_t_3) { - /* "ctabix.pyx":125 + /* "pysam/ctabix.pyx":125 * if mode[0] == 'w': * # open file for writing * raise NotImplementedError("writing to tabix files not implemented" ) # <<<<<<<<<<<<<< * * elif mode[0] == "r": */ - __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_13), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __Pyx_Raise(__pyx_t_1, 0, 0, 0); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_13), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L5; } - /* "ctabix.pyx":127 + /* "pysam/ctabix.pyx":127 * raise NotImplementedError("writing to tabix files not implemented" ) * * elif mode[0] == "r": # <<<<<<<<<<<<<< * # open file for reading * */ - __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - if (__pyx_t_2) { + if (__pyx_t_3) { - /* "ctabix.pyx":130 + /* "pysam/ctabix.pyx":130 * # open file for reading * * if not self.isremote: # <<<<<<<<<<<<<< * if not os.path.exists( filename ): * raise IOError( "file `%s` not found" % filename) */ - __pyx_t_2 = (!__pyx_v_self->isremote); - if (__pyx_t_2) { + __pyx_t_3 = (!__pyx_v_self->isremote); + if (__pyx_t_3) { - /* "ctabix.pyx":131 + /* "pysam/ctabix.pyx":131 * * if not self.isremote: * if not os.path.exists( filename ): # <<<<<<<<<<<<<< @@ -2617,27 +2617,27 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab */ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_filename); - PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_filename); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_filename); __Pyx_GIVEREF(__pyx_v_filename); - __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_7 = (!__pyx_t_2); + __pyx_t_7 = (!__pyx_t_3); if (__pyx_t_7) { - /* "ctabix.pyx":132 + /* "pysam/ctabix.pyx":132 * if not self.isremote: * if not os.path.exists( filename ): * raise IOError( "file `%s` not found" % filename) # <<<<<<<<<<<<<< @@ -2646,14 +2646,14 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab */ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_14), __pyx_v_filename); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_4)); - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4)); + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4)); __Pyx_GIVEREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; - __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -2661,7 +2661,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab } __pyx_L7:; - /* "ctabix.pyx":134 + /* "pysam/ctabix.pyx":134 * raise IOError( "file `%s` not found" % filename) * * if not os.path.exists( filename_index ): # <<<<<<<<<<<<<< @@ -2670,27 +2670,27 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab */ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__exists); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_filename_index); - PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_filename_index); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_filename_index); __Pyx_GIVEREF(__pyx_v_filename_index); - __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_2 = (!__pyx_t_7); - if (__pyx_t_2) { + __pyx_t_3 = (!__pyx_t_7); + if (__pyx_t_3) { - /* "ctabix.pyx":135 + /* "pysam/ctabix.pyx":135 * * if not os.path.exists( filename_index ): * raise IOError( "index `%s` not found" % filename_index) # <<<<<<<<<<<<<< @@ -2699,14 +2699,14 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab */ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_15), __pyx_v_filename_index); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_1)); + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -2717,7 +2717,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab } __pyx_L6:; - /* "ctabix.pyx":138 + /* "pysam/ctabix.pyx":138 * * # open file and load index * self.tabixfile = ti_open( filename, filename_index ) # <<<<<<<<<<<<<< @@ -2731,17 +2731,17 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab } __pyx_L5:; - /* "ctabix.pyx":140 + /* "pysam/ctabix.pyx":140 * self.tabixfile = ti_open( filename, filename_index ) * * if self.tabixfile == NULL: # <<<<<<<<<<<<<< * raise IOError("could not open file `%s`" % filename ) * */ - __pyx_t_2 = (__pyx_v_self->tabixfile == NULL); - if (__pyx_t_2) { + __pyx_t_3 = (__pyx_v_self->tabixfile == NULL); + if (__pyx_t_3) { - /* "ctabix.pyx":141 + /* "pysam/ctabix.pyx":141 * * if self.tabixfile == NULL: * raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<< @@ -2750,14 +2750,14 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab */ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_16), __pyx_v_filename); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_1)); + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -2769,9 +2769,9 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_4); - __Pyx_AddTraceback("ctabix.Tabixfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_filename_index); @@ -2783,21 +2783,21 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tab } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_6ctabix_9Tabixfile_6_parseRegion[] = "Tabixfile._parseRegion(self, reference=None, start=None, end=None, region=None)\nparse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of region, tid, start and end. Region\n is a valid samtools :term:`region` or None if the region\n extends over the whole file.\n\n Note that regions are 1-based, while start,end are python coordinates.\n "; -static PyObject *__pyx_pw_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_9Tabixfile_6_parseRegion[] = "Tabixfile._parseRegion(self, reference=None, start=None, end=None, region=None)\nparse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of region, tid, start and end. Region\n is a valid samtools :term:`region` or None if the region\n extends over the whole file.\n\n Note that regions are 1-based, while start,end are python coordinates.\n "; +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_region = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("_parseRegion (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0}; PyObject* values[4] = {0,0,0,0}; - /* "ctabix.pyx":144 + /* "pysam/ctabix.pyx":144 * * def _parseRegion( self, * reference = None, # <<<<<<<<<<<<<< @@ -2806,7 +2806,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_sel */ values[0] = ((PyObject *)Py_None); - /* "ctabix.pyx":145 + /* "pysam/ctabix.pyx":145 * def _parseRegion( self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -2815,7 +2815,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_sel */ values[1] = ((PyObject *)Py_None); - /* "ctabix.pyx":146 + /* "pysam/ctabix.pyx":146 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -2824,7 +2824,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_sel */ values[2] = ((PyObject *)Py_None); - /* "ctabix.pyx":147 + /* "pysam/ctabix.pyx":147 * start = None, * end = None, * region = None ): # <<<<<<<<<<<<<< @@ -2888,16 +2888,16 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_sel __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("_parseRegion", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.Tabixfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_6_parseRegion(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":143 +/* "pysam/ctabix.pyx":143 * raise IOError("could not open file `%s`" % filename ) * * def _parseRegion( self, # <<<<<<<<<<<<<< @@ -2905,7 +2905,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_7_parseRegion(PyObject *__pyx_v_sel * start = None, */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) { int __pyx_v_rtid; int __pyx_v_rstart; int __pyx_v_rend; @@ -2926,7 +2926,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta __Pyx_RefNannySetupContext("_parseRegion", 0); __Pyx_INCREF(__pyx_v_region); - /* "ctabix.pyx":158 + /* "pysam/ctabix.pyx":158 * Note that regions are 1-based, while start,end are python coordinates. * ''' * ti_lazy_index_load( self.tabixfile ) # <<<<<<<<<<<<<< @@ -2935,7 +2935,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta */ ti_lazy_index_load(__pyx_v_self->tabixfile); - /* "ctabix.pyx":164 + /* "pysam/ctabix.pyx":164 * cdef int rend * cdef int max_pos * max_pos = 2 << 29 # <<<<<<<<<<<<<< @@ -2944,7 +2944,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta */ __pyx_v_max_pos = 1073741824; - /* "ctabix.pyx":166 + /* "pysam/ctabix.pyx":166 * max_pos = 2 << 29 * * rtid = rstart = rend = 0 # <<<<<<<<<<<<<< @@ -2955,7 +2955,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta __pyx_v_rstart = 0; __pyx_v_rend = 0; - /* "ctabix.pyx":169 + /* "pysam/ctabix.pyx":169 * * # translate to a region * if reference: # <<<<<<<<<<<<<< @@ -2965,20 +2965,18 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - /* "ctabix.pyx":170 + /* "pysam/ctabix.pyx":170 * # translate to a region * if reference: * if start != None and end != None: # <<<<<<<<<<<<<< * region = "%s:%i-%i" % (reference, start+1, end) * elif start == None and end != None: */ - __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_1) { - __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __pyx_t_3; @@ -2987,7 +2985,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } if (__pyx_t_4) { - /* "ctabix.pyx":171 + /* "pysam/ctabix.pyx":171 * if reference: * if start != None and end != None: * region = "%s:%i-%i" % (reference, start+1, end) # <<<<<<<<<<<<<< @@ -3016,20 +3014,18 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta goto __pyx_L4; } - /* "ctabix.pyx":172 + /* "pysam/ctabix.pyx":172 * if start != None and end != None: * region = "%s:%i-%i" % (reference, start+1, end) * elif start == None and end != None: # <<<<<<<<<<<<<< * region = "%s:%i-%i" % (reference, 1, end) * elif end == None and start != None: */ - __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_4) { - __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_3 = __pyx_t_1; @@ -3038,7 +3034,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } if (__pyx_t_3) { - /* "ctabix.pyx":173 + /* "pysam/ctabix.pyx":173 * region = "%s:%i-%i" % (reference, start+1, end) * elif start == None and end != None: * region = "%s:%i-%i" % (reference, 1, end) # <<<<<<<<<<<<<< @@ -3065,20 +3061,18 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta goto __pyx_L4; } - /* "ctabix.pyx":174 + /* "pysam/ctabix.pyx":174 * elif start == None and end != None: * region = "%s:%i-%i" % (reference, 1, end) * elif end == None and start != None: # <<<<<<<<<<<<<< * region = "%s:%i-%i" % (reference, start+1, max_pos-1) * else: */ - __pyx_t_5 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_3) { - __pyx_t_5 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_1 = __pyx_t_4; @@ -3087,7 +3081,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } if (__pyx_t_1) { - /* "ctabix.pyx":175 + /* "pysam/ctabix.pyx":175 * region = "%s:%i-%i" % (reference, 1, end) * elif end == None and start != None: * region = "%s:%i-%i" % (reference, start+1, max_pos-1) # <<<<<<<<<<<<<< @@ -3119,7 +3113,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } /*else*/ { - /* "ctabix.pyx":177 + /* "pysam/ctabix.pyx":177 * region = "%s:%i-%i" % (reference, start+1, max_pos-1) * else: * region = reference # <<<<<<<<<<<<<< @@ -3135,7 +3129,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } __pyx_L3:; - /* "ctabix.pyx":179 + /* "pysam/ctabix.pyx":179 * region = reference * * if region: # <<<<<<<<<<<<<< @@ -3145,20 +3139,20 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - /* "ctabix.pyx":180 + /* "pysam/ctabix.pyx":180 * * if region: * region = _force_bytes(region) # <<<<<<<<<<<<<< * ti_parse_region( self.tabixfile.idx, region, * &rtid, &rstart, &rend) */ - __pyx_t_2 = ((PyObject *)__pyx_f_6ctabix__force_bytes(__pyx_v_region)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_6ctabix__force_bytes(__pyx_v_region)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_region); __pyx_v_region = __pyx_t_2; __pyx_t_2 = 0; - /* "ctabix.pyx":181 + /* "pysam/ctabix.pyx":181 * if region: * region = _force_bytes(region) * ti_parse_region( self.tabixfile.idx, region, # <<<<<<<<<<<<<< @@ -3167,7 +3161,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta */ __pyx_t_7 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":182 + /* "pysam/ctabix.pyx":182 * region = _force_bytes(region) * ti_parse_region( self.tabixfile.idx, region, * &rtid, &rstart, &rend) # <<<<<<<<<<<<<< @@ -3176,7 +3170,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta */ ti_parse_region(__pyx_v_self->tabixfile->idx, __pyx_t_7, (&__pyx_v_rtid), (&__pyx_v_rstart), (&__pyx_v_rend)); - /* "ctabix.pyx":183 + /* "pysam/ctabix.pyx":183 * ti_parse_region( self.tabixfile.idx, region, * &rtid, &rstart, &rend) * if rtid < 0: raise ValueError( "invalid region `%s`" % region ) # <<<<<<<<<<<<<< @@ -3202,7 +3196,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } __pyx_L6:; - /* "ctabix.pyx":184 + /* "pysam/ctabix.pyx":184 * &rtid, &rstart, &rend) * if rtid < 0: raise ValueError( "invalid region `%s`" % region ) * if rstart > rend: raise ValueError( 'invalid region: start (%i) > end (%i)' % (rstart, rend) ) # <<<<<<<<<<<<<< @@ -3241,7 +3235,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } __pyx_L7:; - /* "ctabix.pyx":185 + /* "pysam/ctabix.pyx":185 * if rtid < 0: raise ValueError( "invalid region `%s`" % region ) * if rstart > rend: raise ValueError( 'invalid region: start (%i) > end (%i)' % (rstart, rend) ) * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) # <<<<<<<<<<<<<< @@ -3274,7 +3268,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } __pyx_L8:; - /* "ctabix.pyx":186 + /* "pysam/ctabix.pyx":186 * if rstart > rend: raise ValueError( 'invalid region: start (%i) > end (%i)' % (rstart, rend) ) * if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) * if not 0 <= rend < max_pos: raise ValueError( 'end out of range (%i)' % rend ) # <<<<<<<<<<<<<< @@ -3310,7 +3304,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } __pyx_L5:; - /* "ctabix.pyx":188 + /* "pysam/ctabix.pyx":188 * if not 0 <= rend < max_pos: raise ValueError( 'end out of range (%i)' % rend ) * * return region, rtid, rstart, rend # <<<<<<<<<<<<<< @@ -3349,7 +3343,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_8); - __Pyx_AddTraceback("ctabix.Tabixfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_region); @@ -3359,22 +3353,22 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6cta } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_6ctabix_9Tabixfile_8fetch[] = "Tabixfile.fetch(self, reference=None, start=None, end=None, region=None, parser=None)\n\n \n fetch one or more rows in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Without *reference* or *region* all entries will be fetched. \n \n If only *reference* is set, all reads matching on *reference* will be fetched.\n\n If *parser* is None, the results are returned as an unparsed string.\n Otherwise, *parser* is assumed to be a functor that will return parsed \n data (see for example :meth:`asTuple` and :meth:`asGTF`).\n "; -static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_9Tabixfile_8fetch[] = "Tabixfile.fetch(self, reference=None, start=None, end=None, region=None, parser=None)\n\n \n fetch one or more rows in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Without *reference* or *region* all entries will be fetched. \n \n If only *reference* is set, all reads matching on *reference* will be fetched.\n\n If *parser* is None, the results are returned as an unparsed string.\n Otherwise, *parser* is assumed to be a functor that will return parsed \n data (see for example :meth:`asTuple` and :meth:`asGTF`).\n "; +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_region = 0; PyObject *__pyx_v_parser = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__parser,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("fetch (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__parser,0}; PyObject* values[5] = {0,0,0,0,0}; - /* "ctabix.pyx":191 + /* "pysam/ctabix.pyx":191 * * def fetch( self, * reference = None, # <<<<<<<<<<<<<< @@ -3383,7 +3377,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyOb */ values[0] = ((PyObject *)Py_None); - /* "ctabix.pyx":192 + /* "pysam/ctabix.pyx":192 * def fetch( self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -3392,7 +3386,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyOb */ values[1] = ((PyObject *)Py_None); - /* "ctabix.pyx":193 + /* "pysam/ctabix.pyx":193 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -3401,7 +3395,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyOb */ values[2] = ((PyObject *)Py_None); - /* "ctabix.pyx":194 + /* "pysam/ctabix.pyx":194 * start = None, * end = None, * region = None, # <<<<<<<<<<<<<< @@ -3410,7 +3404,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyOb */ values[3] = ((PyObject *)Py_None); - /* "ctabix.pyx":195 + /* "pysam/ctabix.pyx":195 * end = None, * region = None, * parser = None ): # <<<<<<<<<<<<<< @@ -3482,16 +3476,16 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyOb __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 190; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.Tabixfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_8fetch(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_parser); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_parser); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":190 +/* "pysam/ctabix.pyx":190 * return region, rtid, rstart, rend * * def fetch( self, # <<<<<<<<<<<<<< @@ -3499,7 +3493,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyOb * start = None, */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser) { PyObject *__pyx_v_rtid = NULL; PyObject *__pyx_v_rstart = NULL; PyObject *__pyx_v_rend = NULL; @@ -3520,7 +3514,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_RefNannySetupContext("fetch", 0); __Pyx_INCREF(__pyx_v_region); - /* "ctabix.pyx":209 + /* "pysam/ctabix.pyx":209 * data (see for example :meth:`asTuple` and :meth:`asGTF`). * ''' * ti_lazy_index_load( self.tabixfile ) # <<<<<<<<<<<<<< @@ -3529,7 +3523,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab */ ti_lazy_index_load(__pyx_v_self->tabixfile); - /* "ctabix.pyx":211 + /* "pysam/ctabix.pyx":211 * ti_lazy_index_load( self.tabixfile ) * * if not self._isOpen(): # <<<<<<<<<<<<<< @@ -3546,7 +3540,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __pyx_t_4 = (!__pyx_t_3); if (__pyx_t_4) { - /* "ctabix.pyx":212 + /* "pysam/ctabix.pyx":212 * * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< @@ -3562,7 +3556,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab } __pyx_L3:; - /* "ctabix.pyx":214 + /* "pysam/ctabix.pyx":214 * raise ValueError( "I/O operation on closed file" ) * * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<< @@ -3591,22 +3585,23 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) { PyObject* sequence = __pyx_t_5; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 4)) { + if (size > 4) __Pyx_RaiseTooManyValuesError(4); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) { - if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1); __pyx_t_6 = PyTuple_GET_ITEM(sequence, 2); __pyx_t_7 = PyTuple_GET_ITEM(sequence, 3); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 4)) { - if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyList_GET_ITEM(sequence, 0); __pyx_t_2 = PyList_GET_ITEM(sequence, 1); __pyx_t_6 = PyList_GET_ITEM(sequence, 2); @@ -3616,28 +3611,36 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_INCREF(__pyx_t_2); __Pyx_INCREF(__pyx_t_6); __Pyx_INCREF(__pyx_t_7); + #else + Py_ssize_t i; + PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7}; + for (i=0; i < 4; i++) { + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + *(temps[i]) = item; + } + #endif __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - } else { + } else + { Py_ssize_t index = -1; + PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7}; __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext; - index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed; - __Pyx_GOTREF(__pyx_t_1); - index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed; - __Pyx_GOTREF(__pyx_t_2); - index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed; - __Pyx_GOTREF(__pyx_t_6); - index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed; - __Pyx_GOTREF(__pyx_t_7); + for (index=0; index < 4; index++) { + PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed; + __Pyx_GOTREF(item); + *(temps[index]) = item; + } if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = NULL; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; goto __pyx_L5_unpacking_done; __pyx_L4_unpacking_failed:; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_9 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L5_unpacking_done:; } @@ -3651,20 +3654,19 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __pyx_v_rend = __pyx_t_7; __pyx_t_7 = 0; - /* "ctabix.pyx":216 + /* "pysam/ctabix.pyx":216 * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) * * if parser == None: # <<<<<<<<<<<<<< * if region: * return TabixIterator( self, rtid, rstart, rend ) */ - __pyx_t_5 = PyObject_RichCompare(__pyx_v_parser, Py_None, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_v_parser, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_4) { - /* "ctabix.pyx":217 + /* "pysam/ctabix.pyx":217 * * if parser == None: * if region: # <<<<<<<<<<<<<< @@ -3674,7 +3676,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { - /* "ctabix.pyx":218 + /* "pysam/ctabix.pyx":218 * if parser == None: * if region: * return TabixIterator( self, rtid, rstart, rend ) # <<<<<<<<<<<<<< @@ -3696,7 +3698,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_INCREF(__pyx_v_rend); PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_v_rend); __Pyx_GIVEREF(__pyx_v_rend); - __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_6ctabix_TabixIterator)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_6ctabix_TabixIterator)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; __pyx_r = __pyx_t_7; @@ -3706,7 +3708,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab } /*else*/ { - /* "ctabix.pyx":220 + /* "pysam/ctabix.pyx":220 * return TabixIterator( self, rtid, rstart, rend ) * else: * return TabixIterator( self, -1, 0, 0 ) # <<<<<<<<<<<<<< @@ -3728,7 +3730,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_INCREF(__pyx_int_0); PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_int_0); __Pyx_GIVEREF(__pyx_int_0); - __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_6ctabix_TabixIterator)), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_6ctabix_TabixIterator)), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_r = __pyx_t_5; @@ -3740,7 +3742,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab } /*else*/ { - /* "ctabix.pyx":222 + /* "pysam/ctabix.pyx":222 * return TabixIterator( self, -1, 0, 0 ) * else: * if region: # <<<<<<<<<<<<<< @@ -3750,7 +3752,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { - /* "ctabix.pyx":223 + /* "pysam/ctabix.pyx":223 * else: * if region: * return TabixIteratorParsed( self, rtid, rstart, rend, parser ) # <<<<<<<<<<<<<< @@ -3775,7 +3777,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_INCREF(__pyx_v_parser); PyTuple_SET_ITEM(__pyx_t_5, 4, __pyx_v_parser); __Pyx_GIVEREF(__pyx_v_parser); - __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_6ctabix_TabixIteratorParsed)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; __pyx_r = __pyx_t_7; @@ -3785,7 +3787,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab } /*else*/ { - /* "ctabix.pyx":225 + /* "pysam/ctabix.pyx":225 * return TabixIteratorParsed( self, rtid, rstart, rend, parser ) * else: * return TabixIteratorParsed( self, -1, 0, 0, parser ) # <<<<<<<<<<<<<< @@ -3810,7 +3812,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_INCREF(__pyx_v_parser); PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_v_parser); __Pyx_GIVEREF(__pyx_v_parser); - __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_6ctabix_TabixIteratorParsed)), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed)), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_r = __pyx_t_5; @@ -3830,7 +3832,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_7); __Pyx_XDECREF(__pyx_t_8); - __Pyx_AddTraceback("ctabix.Tabixfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_rtid); @@ -3843,17 +3845,17 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_8filename_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_8filename_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_8filename___get__(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_8filename___get__(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":234 +/* "pysam/ctabix.pyx":234 * property filename: * '''filename associated with this object.''' * def __get__(self): # <<<<<<<<<<<<<< @@ -3861,7 +3863,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_8filename_1__get__(PyObject *__pyx_ * return self._filename */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3873,7 +3875,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "ctabix.pyx":235 + /* "pysam/ctabix.pyx":235 * '''filename associated with this object.''' * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< @@ -3898,7 +3900,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_ } __pyx_L3:; - /* "ctabix.pyx":236 + /* "pysam/ctabix.pyx":236 * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) * return self._filename # <<<<<<<<<<<<<< @@ -3917,7 +3919,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.Tabixfile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3926,17 +3928,17 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_ } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_6header_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_6header_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_6header___get__(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_6header___get__(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":246 +/* "pysam/ctabix.pyx":246 * ''' * * def __get__( self ): # <<<<<<<<<<<<<< @@ -3944,7 +3946,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_6header_1__get__(PyObject *__pyx_v_ * */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3954,7 +3956,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6c int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "ctabix.pyx":247 + /* "pysam/ctabix.pyx":247 * * def __get__( self ): * return TabixHeaderIterator( self ) # <<<<<<<<<<<<<< @@ -3967,7 +3969,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6c __Pyx_INCREF(((PyObject *)__pyx_v_self)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); - __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_6ctabix_TabixHeaderIterator)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_r = __pyx_t_2; @@ -3979,7 +3981,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6c __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.Tabixfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3988,17 +3990,17 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6c } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_7contigs_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_7contigs_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_7contigs_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_7contigs_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_7contigs___get__(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":251 +/* "pysam/ctabix.pyx":251 * property contigs: * '''chromosome names''' * def __get__(self): # <<<<<<<<<<<<<< @@ -4006,7 +4008,7 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_7contigs_1__get__(PyObject *__pyx_v * cdef int nsequences */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self) { char **__pyx_v_sequences; int __pyx_v_nsequences; int __pyx_v_x; @@ -4021,7 +4023,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "ctabix.pyx":255 + /* "pysam/ctabix.pyx":255 * cdef int nsequences * * ti_lazy_index_load( self.tabixfile ) # <<<<<<<<<<<<<< @@ -4030,7 +4032,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 */ ti_lazy_index_load(__pyx_v_self->tabixfile); - /* "ctabix.pyx":256 + /* "pysam/ctabix.pyx":256 * * ti_lazy_index_load( self.tabixfile ) * sequences = ti_seqname( self.tabixfile.idx, &nsequences ) # <<<<<<<<<<<<<< @@ -4039,7 +4041,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 */ __pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences)); - /* "ctabix.pyx":258 + /* "pysam/ctabix.pyx":258 * sequences = ti_seqname( self.tabixfile.idx, &nsequences ) * cdef int x * result = [] # <<<<<<<<<<<<<< @@ -4051,7 +4053,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 __pyx_v_result = __pyx_t_1; __pyx_t_1 = 0; - /* "ctabix.pyx":259 + /* "pysam/ctabix.pyx":259 * cdef int x * result = [] * for x from 0 <= x < nsequences: # <<<<<<<<<<<<<< @@ -4061,7 +4063,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 __pyx_t_2 = __pyx_v_nsequences; for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_2; __pyx_v_x++) { - /* "ctabix.pyx":260 + /* "pysam/ctabix.pyx":260 * result = [] * for x from 0 <= x < nsequences: * result.append( sequences[x] ) # <<<<<<<<<<<<<< @@ -4074,7 +4076,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; } - /* "ctabix.pyx":261 + /* "pysam/ctabix.pyx":261 * for x from 0 <= x < nsequences: * result.append( sequences[x] ) * return result # <<<<<<<<<<<<<< @@ -4090,7 +4092,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.Tabixfile.contigs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.Tabixfile.contigs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_result); @@ -4100,18 +4102,18 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6 } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_9Tabixfile_11close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_6ctabix_9Tabixfile_10close[] = "Tabixfile.close(self)\n\n closes the :class:`pysam.Tabixfile`."; -static PyObject *__pyx_pw_6ctabix_9Tabixfile_11close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_11close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_9Tabixfile_10close[] = "Tabixfile.close(self)\n\n closes the :class:`pysam.Tabixfile`."; +static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_11close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("close (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_9Tabixfile_10close(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_10close(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":263 +/* "pysam/ctabix.pyx":263 * return result * * def close( self ): # <<<<<<<<<<<<<< @@ -4119,13 +4121,13 @@ static PyObject *__pyx_pw_6ctabix_9Tabixfile_11close(PyObject *__pyx_v_self, CYT * closes the :class:`pysam.Tabixfile`.''' */ -static PyObject *__pyx_pf_6ctabix_9Tabixfile_10close(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_10close(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_RefNannySetupContext("close", 0); - /* "ctabix.pyx":266 + /* "pysam/ctabix.pyx":266 * ''' * closes the :class:`pysam.Tabixfile`.''' * if self.tabixfile != NULL: # <<<<<<<<<<<<<< @@ -4135,7 +4137,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_10close(struct __pyx_obj_6ctabix_Ta __pyx_t_1 = (__pyx_v_self->tabixfile != NULL); if (__pyx_t_1) { - /* "ctabix.pyx":267 + /* "pysam/ctabix.pyx":267 * closes the :class:`pysam.Tabixfile`.''' * if self.tabixfile != NULL: * ti_close( self.tabixfile ) # <<<<<<<<<<<<<< @@ -4144,7 +4146,7 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_10close(struct __pyx_obj_6ctabix_Ta */ ti_close(__pyx_v_self->tabixfile); - /* "ctabix.pyx":268 + /* "pysam/ctabix.pyx":268 * if self.tabixfile != NULL: * ti_close( self.tabixfile ) * self.tabixfile = NULL # <<<<<<<<<<<<<< @@ -4163,15 +4165,15 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_10close(struct __pyx_obj_6ctabix_Ta } /* Python wrapper */ -static void __pyx_pw_6ctabix_9Tabixfile_13__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_6ctabix_9Tabixfile_13__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pw_5pysam_6ctabix_9Tabixfile_13__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_5pysam_6ctabix_9Tabixfile_13__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(((struct __pyx_obj_6ctabix_Tabixfile *)__pyx_v_self)); + __pyx_pf_5pysam_6ctabix_9Tabixfile_12__dealloc__(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } -/* "ctabix.pyx":270 +/* "pysam/ctabix.pyx":270 * self.tabixfile = NULL * * def __dealloc__( self ): # <<<<<<<<<<<<<< @@ -4179,12 +4181,12 @@ static void __pyx_pw_6ctabix_9Tabixfile_13__dealloc__(PyObject *__pyx_v_self) { * # note: no doc string */ -static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self) { +static void __pyx_pf_5pysam_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self) { __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_RefNannySetupContext("__dealloc__", 0); - /* "ctabix.pyx":274 + /* "pysam/ctabix.pyx":274 * # note: no doc string * # note: __del__ is not called. * if self.tabixfile != NULL: # <<<<<<<<<<<<<< @@ -4194,7 +4196,7 @@ static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_T __pyx_t_1 = (__pyx_v_self->tabixfile != NULL); if (__pyx_t_1) { - /* "ctabix.pyx":275 + /* "pysam/ctabix.pyx":275 * # note: __del__ is not called. * if self.tabixfile != NULL: * ti_close( self.tabixfile ) # <<<<<<<<<<<<<< @@ -4203,7 +4205,7 @@ static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_T */ ti_close(__pyx_v_self->tabixfile); - /* "ctabix.pyx":276 + /* "pysam/ctabix.pyx":276 * if self.tabixfile != NULL: * ti_close( self.tabixfile ) * self.tabixfile = NULL # <<<<<<<<<<<<<< @@ -4215,7 +4217,7 @@ static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_T } __pyx_L3:; - /* "ctabix.pyx":277 + /* "pysam/ctabix.pyx":277 * ti_close( self.tabixfile ) * self.tabixfile = NULL * if self._filename != NULL: free( self._filename ) # <<<<<<<<<<<<<< @@ -4233,17 +4235,17 @@ static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_T } /* Python wrapper */ -static int __pyx_pw_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { - struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile = 0; +static int __pyx_pw_5pysam_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile = 0; int __pyx_v_tid; int __pyx_v_start; int __pyx_v_end; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,0}; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,0}; PyObject* values[4] = {0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -4259,24 +4261,20 @@ static int __pyx_pw_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, P kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); - if (likely(values[3])) kw_args--; + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -4292,7 +4290,7 @@ static int __pyx_pw_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, P values[2] = PyTuple_GET_ITEM(__pyx_args, 2); values[3] = PyTuple_GET_ITEM(__pyx_args, 3); } - __pyx_v_tabixfile = ((struct __pyx_obj_6ctabix_Tabixfile *)values[0]); + __pyx_v_tabixfile = ((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)values[0]); __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_start = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L3_error;} @@ -4301,12 +4299,12 @@ static int __pyx_pw_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, P __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.TabixIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_tabixfile), __pyx_ptype_6ctabix_Tabixfile, 1, "tabixfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_6ctabix_13TabixIterator___cinit__(((struct __pyx_obj_6ctabix_TabixIterator *)__pyx_v_self), __pyx_v_tabixfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_tabixfile), __pyx_ptype_5pysam_6ctabix_Tabixfile, 1, "tabixfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(((struct __pyx_obj_5pysam_6ctabix_TabixIterator *)__pyx_v_self), __pyx_v_tabixfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end); goto __pyx_L0; __pyx_L1_error:; __pyx_r = -1; @@ -4315,7 +4313,7 @@ static int __pyx_pw_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, P return __pyx_r; } -/* "ctabix.pyx":284 +/* "pysam/ctabix.pyx":284 * """ * * def __cinit__(self, Tabixfile tabixfile, # <<<<<<<<<<<<<< @@ -4323,18 +4321,19 @@ static int __pyx_pw_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_self, P * */ -static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end) { +static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end) { int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; int __pyx_t_3; + tabix_t *__pyx_t_4; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "ctabix.pyx":287 + /* "pysam/ctabix.pyx":287 * int tid, int start, int end ): * * assert tabixfile._isOpen() # <<<<<<<<<<<<<< @@ -4355,16 +4354,17 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T } #endif - /* "ctabix.pyx":291 + /* "pysam/ctabix.pyx":291 * # makes sure that samfile stays alive as long as the * # iterator is alive. * self.tabixfile = tabixfile.tabixfile # <<<<<<<<<<<<<< * * if tid < 0: */ - __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile; + __pyx_t_4 = __pyx_v_tabixfile->tabixfile; + __pyx_v_self->tabixfile = __pyx_t_4; - /* "ctabix.pyx":293 + /* "pysam/ctabix.pyx":293 * self.tabixfile = tabixfile.tabixfile * * if tid < 0: # <<<<<<<<<<<<<< @@ -4374,7 +4374,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T __pyx_t_3 = (__pyx_v_tid < 0); if (__pyx_t_3) { - /* "ctabix.pyx":296 + /* "pysam/ctabix.pyx":296 * # seek to start of file to ensure iteration is over * # all entries. * bgzf_seek( self.tabixfile.fp, 0, 0) # <<<<<<<<<<<<<< @@ -4383,7 +4383,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T */ bgzf_seek(__pyx_v_self->tabixfile->fp, 0, 0); - /* "ctabix.pyx":297 + /* "pysam/ctabix.pyx":297 * # all entries. * bgzf_seek( self.tabixfile.fp, 0, 0) * self.iterator = ti_iter_first() # <<<<<<<<<<<<<< @@ -4395,7 +4395,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T } /*else*/ { - /* "ctabix.pyx":299 + /* "pysam/ctabix.pyx":299 * self.iterator = ti_iter_first() * else: * self.iterator = ti_queryi(self.tabixfile, tid, start, end) # <<<<<<<<<<<<<< @@ -4406,7 +4406,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T } __pyx_L3:; - /* "ctabix.pyx":301 + /* "pysam/ctabix.pyx":301 * self.iterator = ti_queryi(self.tabixfile, tid, start, end) * * if self.iterator == NULL: # <<<<<<<<<<<<<< @@ -4416,7 +4416,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T __pyx_t_3 = (((void *)__pyx_v_self->iterator) == NULL); if (__pyx_t_3) { - /* "ctabix.pyx":302 + /* "pysam/ctabix.pyx":302 * * if self.iterator == NULL: * raise ValueError("malformatted query or wrong sequence name.\n") # <<<<<<<<<<<<<< @@ -4437,7 +4437,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.TabixIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -4445,17 +4445,17 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_13TabixIterator_2__iter__(((struct __pyx_obj_6ctabix_TabixIterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_13TabixIterator_2__iter__(((struct __pyx_obj_5pysam_6ctabix_TabixIterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":304 +/* "pysam/ctabix.pyx":304 * raise ValueError("malformatted query or wrong sequence name.\n") * * def __iter__(self): # <<<<<<<<<<<<<< @@ -4463,12 +4463,12 @@ static PyObject *__pyx_pw_6ctabix_13TabixIterator_3__iter__(PyObject *__pyx_v_se * */ -static PyObject *__pyx_pf_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__", 0); - /* "ctabix.pyx":305 + /* "pysam/ctabix.pyx":305 * * def __iter__(self): * return self # <<<<<<<<<<<<<< @@ -4488,19 +4488,21 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_6ct } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_6ctabix_13TabixIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; -struct wrapperbase __pyx_wrapperbase_6ctabix_13TabixIterator_4__next__; -static PyObject *__pyx_pw_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; +#if CYTHON_COMPILING_IN_CPYTHON +struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__; +#endif +static PyObject *__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_13TabixIterator_4__next__(((struct __pyx_obj_6ctabix_TabixIterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__(((struct __pyx_obj_5pysam_6ctabix_TabixIterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":307 +/* "pysam/ctabix.pyx":307 * return self * * def __next__(self): # <<<<<<<<<<<<<< @@ -4508,7 +4510,7 @@ static PyObject *__pyx_pw_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_se * */ -static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self) { char *__pyx_v_s; int __pyx_v_len; PyObject *__pyx_v_retval = NULL; @@ -4521,7 +4523,7 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ct int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "ctabix.pyx":320 + /* "pysam/ctabix.pyx":320 * * # simply use '#' for now. * while 1: # <<<<<<<<<<<<<< @@ -4531,7 +4533,7 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ct while (1) { if (!1) break; - /* "ctabix.pyx":321 + /* "pysam/ctabix.pyx":321 * # simply use '#' for now. * while 1: * s = ti_read(self.tabixfile, self.iterator, &len) # <<<<<<<<<<<<<< @@ -4540,7 +4542,7 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ct */ __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); - /* "ctabix.pyx":322 + /* "pysam/ctabix.pyx":322 * while 1: * s = ti_read(self.tabixfile, self.iterator, &len) * if s == NULL: raise StopIteration # <<<<<<<<<<<<<< @@ -4555,7 +4557,7 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ct } __pyx_L5:; - /* "ctabix.pyx":323 + /* "pysam/ctabix.pyx":323 * s = ti_read(self.tabixfile, self.iterator, &len) * if s == NULL: raise StopIteration * if s[0] != '#': break # <<<<<<<<<<<<<< @@ -4571,19 +4573,19 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ct } __pyx_L4_break:; - /* "ctabix.pyx":325 + /* "pysam/ctabix.pyx":325 * if s[0] != '#': break * * retval = _charptr_to_str( s ) # <<<<<<<<<<<<<< * return retval * */ - __pyx_t_2 = __pyx_f_6ctabix__charptr_to_str(__pyx_v_s); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_5pysam_6ctabix__charptr_to_str(__pyx_v_s); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_v_retval = __pyx_t_2; __pyx_t_2 = 0; - /* "ctabix.pyx":326 + /* "pysam/ctabix.pyx":326 * * retval = _charptr_to_str( s ) * return retval # <<<<<<<<<<<<<< @@ -4599,7 +4601,7 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ct goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.TabixIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_retval); @@ -4609,15 +4611,15 @@ static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ct } /* Python wrapper */ -static void __pyx_pw_6ctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_6ctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pw_5pysam_6ctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_5pysam_6ctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_6ctabix_13TabixIterator_6__dealloc__(((struct __pyx_obj_6ctabix_TabixIterator *)__pyx_v_self)); + __pyx_pf_5pysam_6ctabix_13TabixIterator_6__dealloc__(((struct __pyx_obj_5pysam_6ctabix_TabixIterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } -/* "ctabix.pyx":328 +/* "pysam/ctabix.pyx":328 * return retval * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -4625,12 +4627,12 @@ static void __pyx_pw_6ctabix_13TabixIterator_7__dealloc__(PyObject *__pyx_v_self * ti_iter_destroy(self.iterator) */ -static void __pyx_pf_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self) { +static void __pyx_pf_5pysam_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self) { __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_RefNannySetupContext("__dealloc__", 0); - /* "ctabix.pyx":329 + /* "pysam/ctabix.pyx":329 * * def __dealloc__(self): * if self.iterator != NULL: # <<<<<<<<<<<<<< @@ -4640,7 +4642,7 @@ static void __pyx_pf_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_6ctab __pyx_t_1 = (((void *)__pyx_v_self->iterator) != NULL); if (__pyx_t_1) { - /* "ctabix.pyx":330 + /* "pysam/ctabix.pyx":330 * def __dealloc__(self): * if self.iterator != NULL: * ti_iter_destroy(self.iterator) # <<<<<<<<<<<<<< @@ -4656,14 +4658,14 @@ static void __pyx_pf_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_6ctab } /* Python wrapper */ -static int __pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { - struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,0}; +static int __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,0}; PyObject* values[1] = {0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -4676,8 +4678,7 @@ static int __pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_s kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; } if (unlikely(kw_args > 0)) { @@ -4688,18 +4689,18 @@ static int __pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_s } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); } - __pyx_v_tabixfile = ((struct __pyx_obj_6ctabix_Tabixfile *)values[0]); + __pyx_v_tabixfile = ((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)values[0]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.TabixHeaderIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixHeaderIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_tabixfile), __pyx_ptype_6ctabix_Tabixfile, 1, "tabixfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(((struct __pyx_obj_6ctabix_TabixHeaderIterator *)__pyx_v_self), __pyx_v_tabixfile); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_tabixfile), __pyx_ptype_5pysam_6ctabix_Tabixfile, 1, "tabixfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(((struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *)__pyx_v_self), __pyx_v_tabixfile); goto __pyx_L0; __pyx_L1_error:; __pyx_r = -1; @@ -4708,7 +4709,7 @@ static int __pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_s return __pyx_r; } -/* "ctabix.pyx":336 +/* "pysam/ctabix.pyx":336 * """ * * def __cinit__(self, Tabixfile tabixfile ): # <<<<<<<<<<<<<< @@ -4716,18 +4717,19 @@ static int __pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_s * assert tabixfile._isOpen() */ -static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile) { +static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile) { int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; int __pyx_t_3; + tabix_t *__pyx_t_4; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "ctabix.pyx":338 + /* "pysam/ctabix.pyx":338 * def __cinit__(self, Tabixfile tabixfile ): * * assert tabixfile._isOpen() # <<<<<<<<<<<<<< @@ -4748,16 +4750,17 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct } #endif - /* "ctabix.pyx":342 + /* "pysam/ctabix.pyx":342 * # makes sure that samfile stays alive as long as the * # iterator is alive. * self.tabixfile = tabixfile.tabixfile # <<<<<<<<<<<<<< * * self.iterator = ti_query(self.tabixfile, NULL, 0, 0) */ - __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile; + __pyx_t_4 = __pyx_v_tabixfile->tabixfile; + __pyx_v_self->tabixfile = __pyx_t_4; - /* "ctabix.pyx":344 + /* "pysam/ctabix.pyx":344 * self.tabixfile = tabixfile.tabixfile * * self.iterator = ti_query(self.tabixfile, NULL, 0, 0) # <<<<<<<<<<<<<< @@ -4766,7 +4769,7 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct */ __pyx_v_self->iterator = ti_query(__pyx_v_self->tabixfile, NULL, 0, 0); - /* "ctabix.pyx":346 + /* "pysam/ctabix.pyx":346 * self.iterator = ti_query(self.tabixfile, NULL, 0, 0) * * if self.iterator == NULL: # <<<<<<<<<<<<<< @@ -4776,7 +4779,7 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct __pyx_t_3 = (((void *)__pyx_v_self->iterator) == NULL); if (__pyx_t_3) { - /* "ctabix.pyx":347 + /* "pysam/ctabix.pyx":347 * * if self.iterator == NULL: * raise ValueError("can't open header.\n") # <<<<<<<<<<<<<< @@ -4797,7 +4800,7 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.TabixHeaderIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixHeaderIterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -4805,17 +4808,17 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_19TabixHeaderIterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_19TabixHeaderIterator_3__iter__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_19TabixHeaderIterator_2__iter__(((struct __pyx_obj_6ctabix_TabixHeaderIterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(((struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":349 +/* "pysam/ctabix.pyx":349 * raise ValueError("can't open header.\n") * * def __iter__(self): # <<<<<<<<<<<<<< @@ -4823,12 +4826,12 @@ static PyObject *__pyx_pw_6ctabix_19TabixHeaderIterator_3__iter__(PyObject *__py * */ -static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__", 0); - /* "ctabix.pyx":350 + /* "pysam/ctabix.pyx":350 * * def __iter__(self): * return self # <<<<<<<<<<<<<< @@ -4848,19 +4851,21 @@ static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_o } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_6ctabix_19TabixHeaderIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; -struct wrapperbase __pyx_wrapperbase_6ctabix_19TabixHeaderIterator_4__next__; -static PyObject *__pyx_pw_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; +#if CYTHON_COMPILING_IN_CPYTHON +struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__; +#endif +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(((struct __pyx_obj_6ctabix_TabixHeaderIterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(((struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":352 +/* "pysam/ctabix.pyx":352 * return self * * def __next__(self): # <<<<<<<<<<<<<< @@ -4868,7 +4873,7 @@ static PyObject *__pyx_pw_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__py * */ -static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self) { char *__pyx_v_s; int __pyx_v_len; PyObject *__pyx_r = NULL; @@ -4880,7 +4885,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_o int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "ctabix.pyx":363 + /* "pysam/ctabix.pyx":363 * # Getting the metachar is a pain as ti_index_t is incomplete type. * # simply use '#' for now. * s = ti_read(self.tabixfile, self.iterator, &len) # <<<<<<<<<<<<<< @@ -4889,7 +4894,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_o */ __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); - /* "ctabix.pyx":364 + /* "pysam/ctabix.pyx":364 * # simply use '#' for now. * s = ti_read(self.tabixfile, self.iterator, &len) * if s == NULL: raise StopIteration # <<<<<<<<<<<<<< @@ -4904,7 +4909,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_o } __pyx_L3:; - /* "ctabix.pyx":366 + /* "pysam/ctabix.pyx":366 * if s == NULL: raise StopIteration * # stop at first non-header line * if s[0] != '#': raise StopIteration # <<<<<<<<<<<<<< @@ -4919,7 +4924,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_o } __pyx_L4:; - /* "ctabix.pyx":368 + /* "pysam/ctabix.pyx":368 * if s[0] != '#': raise StopIteration * * return s # <<<<<<<<<<<<<< @@ -4937,7 +4942,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_o goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.TabixHeaderIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixHeaderIterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -4946,15 +4951,15 @@ static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_o } /* Python wrapper */ -static void __pyx_pw_6ctabix_19TabixHeaderIterator_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_6ctabix_19TabixHeaderIterator_7__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_6ctabix_19TabixHeaderIterator_6__dealloc__(((struct __pyx_obj_6ctabix_TabixHeaderIterator *)__pyx_v_self)); + __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_6__dealloc__(((struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } -/* "ctabix.pyx":370 +/* "pysam/ctabix.pyx":370 * return s * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -4962,12 +4967,12 @@ static void __pyx_pw_6ctabix_19TabixHeaderIterator_7__dealloc__(PyObject *__pyx_ * ti_iter_destroy(self.iterator) */ -static void __pyx_pf_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self) { +static void __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self) { __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_RefNannySetupContext("__dealloc__", 0); - /* "ctabix.pyx":371 + /* "pysam/ctabix.pyx":371 * * def __dealloc__(self): * if self.iterator != NULL: # <<<<<<<<<<<<<< @@ -4977,7 +4982,7 @@ static void __pyx_pf_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj __pyx_t_1 = (((void *)__pyx_v_self->iterator) != NULL); if (__pyx_t_1) { - /* "ctabix.pyx":372 + /* "pysam/ctabix.pyx":372 * def __dealloc__(self): * if self.iterator != NULL: * ti_iter_destroy(self.iterator) # <<<<<<<<<<<<<< @@ -4993,15 +4998,15 @@ static void __pyx_pf_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { char *__pyx_v_buffer; int __pyx_v_len; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__call__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -5015,12 +5020,10 @@ static PyObject *__pyx_pw_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyO kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -5041,16 +5044,16 @@ static PyObject *__pyx_pw_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyO __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.asTuple.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asTuple.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_7asTuple___call__(((struct __pyx_obj_6ctabix_asTuple *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); + __pyx_r = __pyx_pf_5pysam_6ctabix_7asTuple___call__(((struct __pyx_obj_5pysam_6ctabix_asTuple *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":386 +/* "pysam/ctabix.pyx":386 * Access is by numeric index. * ''' * def __call__(self, char * buffer, int len): # <<<<<<<<<<<<<< @@ -5058,8 +5061,8 @@ static PyObject *__pyx_pw_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyO * r = TabProxies.TupleProxy() */ -static PyObject *__pyx_pf_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { - struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_r = 0; +static PyObject *__pyx_pf_5pysam_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { + struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_r = 0; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -5068,30 +5071,30 @@ static PyObject *__pyx_pf_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_o int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__call__", 0); - /* "ctabix.pyx":388 + /* "pysam/ctabix.pyx":388 * def __call__(self, char * buffer, int len): * cdef TabProxies.TupleProxy r * r = TabProxies.TupleProxy() # <<<<<<<<<<<<<< * # need to copy - there were some * # persistence issues with "present" */ - __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_TupleProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_TupleProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_v_r = ((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_t_1); + __pyx_v_r = ((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":391 + /* "pysam/ctabix.pyx":391 * # need to copy - there were some * # persistence issues with "present" * r.copy( buffer, len ) # <<<<<<<<<<<<<< * return r * */ - __pyx_t_1 = ((struct __pyx_vtabstruct_10TabProxies_TupleProxy *)__pyx_v_r->__pyx_vtab)->copy(__pyx_v_r, __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *)__pyx_v_r->__pyx_vtab)->copy(__pyx_v_r, __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":392 + /* "pysam/ctabix.pyx":392 * # persistence issues with "present" * r.copy( buffer, len ) * return r # <<<<<<<<<<<<<< @@ -5107,7 +5110,7 @@ static PyObject *__pyx_pf_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_o goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.asTuple.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asTuple.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_r); @@ -5117,15 +5120,15 @@ static PyObject *__pyx_pf_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_o } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { char *__pyx_v_buffer; int __pyx_v_len; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__call__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -5139,12 +5142,10 @@ static PyObject *__pyx_pw_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -5165,16 +5166,16 @@ static PyObject *__pyx_pw_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.asGTF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asGTF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_5asGTF___call__(((struct __pyx_obj_6ctabix_asGTF *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); + __pyx_r = __pyx_pf_5pysam_6ctabix_5asGTF___call__(((struct __pyx_obj_5pysam_6ctabix_asGTF *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":425 +/* "pysam/ctabix.pyx":425 * * ''' * def __call__(self, char * buffer, int len): # <<<<<<<<<<<<<< @@ -5182,8 +5183,8 @@ static PyObject *__pyx_pw_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObj * r = TabProxies.GTFProxy() */ -static PyObject *__pyx_pf_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { - struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_r = 0; +static PyObject *__pyx_pf_5pysam_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { + struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_r = 0; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -5192,30 +5193,30 @@ static PyObject *__pyx_pf_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__call__", 0); - /* "ctabix.pyx":427 + /* "pysam/ctabix.pyx":427 * def __call__(self, char * buffer, int len): * cdef TabProxies.GTFProxy r * r = TabProxies.GTFProxy() # <<<<<<<<<<<<<< * r.copy( buffer, len ) * return r */ - __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_GTFProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_GTFProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_v_r = ((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_t_1); + __pyx_v_r = ((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":428 + /* "pysam/ctabix.pyx":428 * cdef TabProxies.GTFProxy r * r = TabProxies.GTFProxy() * r.copy( buffer, len ) # <<<<<<<<<<<<<< * return r * */ - __pyx_t_1 = ((struct __pyx_vtabstruct_10TabProxies_GTFProxy *)__pyx_v_r->__pyx_base.__pyx_vtab)->__pyx_base.copy(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *)__pyx_v_r->__pyx_base.__pyx_vtab)->__pyx_base.copy(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":429 + /* "pysam/ctabix.pyx":429 * r = TabProxies.GTFProxy() * r.copy( buffer, len ) * return r # <<<<<<<<<<<<<< @@ -5231,7 +5232,7 @@ static PyObject *__pyx_pf_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.asGTF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asGTF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_r); @@ -5241,15 +5242,15 @@ static PyObject *__pyx_pf_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { char *__pyx_v_buffer; int __pyx_v_len; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__call__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -5263,12 +5264,10 @@ static PyObject *__pyx_pw_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -5289,16 +5288,16 @@ static PyObject *__pyx_pw_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.asBed.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asBed.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_5asBed___call__(((struct __pyx_obj_6ctabix_asBed *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); + __pyx_r = __pyx_pf_5pysam_6ctabix_5asBed___call__(((struct __pyx_obj_5pysam_6ctabix_asBed *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":465 +/* "pysam/ctabix.pyx":465 * * ''' * def __call__(self, char * buffer, int len): # <<<<<<<<<<<<<< @@ -5306,8 +5305,8 @@ static PyObject *__pyx_pw_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObj * r = TabProxies.BedProxy() */ -static PyObject *__pyx_pf_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { - struct __pyx_obj_10TabProxies_BedProxy *__pyx_v_r = 0; +static PyObject *__pyx_pf_5pysam_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { + struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_r = 0; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -5316,30 +5315,30 @@ static PyObject *__pyx_pf_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__call__", 0); - /* "ctabix.pyx":467 + /* "pysam/ctabix.pyx":467 * def __call__(self, char * buffer, int len): * cdef TabProxies.BedProxy r * r = TabProxies.BedProxy() # <<<<<<<<<<<<<< * r.copy( buffer, len ) * return r */ - __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_BedProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_BedProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_v_r = ((struct __pyx_obj_10TabProxies_BedProxy *)__pyx_t_1); + __pyx_v_r = ((struct __pyx_obj_5pysam_10TabProxies_BedProxy *)__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":468 + /* "pysam/ctabix.pyx":468 * cdef TabProxies.BedProxy r * r = TabProxies.BedProxy() * r.copy( buffer, len ) # <<<<<<<<<<<<<< * return r * */ - __pyx_t_1 = ((struct __pyx_vtabstruct_10TabProxies_BedProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":469 + /* "pysam/ctabix.pyx":469 * r = TabProxies.BedProxy() * r.copy( buffer, len ) * return r # <<<<<<<<<<<<<< @@ -5355,7 +5354,7 @@ static PyObject *__pyx_pf_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.asBed.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asBed.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_r); @@ -5365,15 +5364,15 @@ static PyObject *__pyx_pf_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { char *__pyx_v_buffer; int __pyx_v_len; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__call__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -5387,12 +5386,10 @@ static PyObject *__pyx_pw_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -5413,16 +5410,16 @@ static PyObject *__pyx_pw_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.asVCF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asVCF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_5asVCF___call__(((struct __pyx_obj_6ctabix_asVCF *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); + __pyx_r = __pyx_pf_5pysam_6ctabix_5asVCF___call__(((struct __pyx_obj_5pysam_6ctabix_asVCF *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":501 +/* "pysam/ctabix.pyx":501 * * ''' * def __call__(self, char * buffer, int len ): # <<<<<<<<<<<<<< @@ -5430,8 +5427,8 @@ static PyObject *__pyx_pw_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObj * r = TabProxies.VCFProxy() */ -static PyObject *__pyx_pf_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { - struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_r = 0; +static PyObject *__pyx_pf_5pysam_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { + struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_r = 0; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -5440,30 +5437,30 @@ static PyObject *__pyx_pf_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__call__", 0); - /* "ctabix.pyx":503 + /* "pysam/ctabix.pyx":503 * def __call__(self, char * buffer, int len ): * cdef TabProxies.VCFProxy r * r = TabProxies.VCFProxy() # <<<<<<<<<<<<<< * r.copy( buffer, len ) * return r */ - __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_VCFProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_VCFProxy)), ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_v_r = ((struct __pyx_obj_10TabProxies_VCFProxy *)__pyx_t_1); + __pyx_v_r = ((struct __pyx_obj_5pysam_10TabProxies_VCFProxy *)__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":504 + /* "pysam/ctabix.pyx":504 * cdef TabProxies.VCFProxy r * r = TabProxies.VCFProxy() * r.copy( buffer, len ) # <<<<<<<<<<<<<< * return r * */ - __pyx_t_1 = ((struct __pyx_vtabstruct_10TabProxies_VCFProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *)__pyx_v_r->__pyx_base.__pyx_base.__pyx_vtab)->__pyx_base.__pyx_base.copy(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":505 + /* "pysam/ctabix.pyx":505 * r = TabProxies.VCFProxy() * r.copy( buffer, len ) * return r # <<<<<<<<<<<<<< @@ -5479,7 +5476,7 @@ static PyObject *__pyx_pf_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.asVCF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.asVCF.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_r); @@ -5489,18 +5486,18 @@ static PyObject *__pyx_pf_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj } /* Python wrapper */ -static int __pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { - struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile = 0; +static int __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { + struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile = 0; int __pyx_v_tid; int __pyx_v_start; int __pyx_v_end; - struct __pyx_obj_6ctabix_Parser *__pyx_v_parser = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__parser,0}; + struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__parser,0}; PyObject* values[5] = {0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -5517,30 +5514,25 @@ static int __pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_s kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); - if (likely(values[3])) kw_args--; + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: - values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser); - if (likely(values[4])) kw_args--; + if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -5557,23 +5549,23 @@ static int __pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_s values[3] = PyTuple_GET_ITEM(__pyx_args, 3); values[4] = PyTuple_GET_ITEM(__pyx_args, 4); } - __pyx_v_tabixfile = ((struct __pyx_obj_6ctabix_Tabixfile *)values[0]); + __pyx_v_tabixfile = ((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)values[0]); __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_start = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_parser = ((struct __pyx_obj_6ctabix_Parser *)values[4]); + __pyx_v_parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)values[4]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.TabixIteratorParsed.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixIteratorParsed.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_tabixfile), __pyx_ptype_6ctabix_Tabixfile, 1, "tabixfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_6ctabix_Parser, 1, "parser", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(((struct __pyx_obj_6ctabix_TabixIteratorParsed *)__pyx_v_self), __pyx_v_tabixfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end, __pyx_v_parser); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_tabixfile), __pyx_ptype_5pysam_6ctabix_Tabixfile, 1, "tabixfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_5pysam_6ctabix_Parser, 1, "parser", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)__pyx_v_self), __pyx_v_tabixfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end, __pyx_v_parser); goto __pyx_L0; __pyx_L1_error:; __pyx_r = -1; @@ -5582,7 +5574,7 @@ static int __pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_s return __pyx_r; } -/* "ctabix.pyx":516 +/* "pysam/ctabix.pyx":516 * """ * * def __cinit__(self, # <<<<<<<<<<<<<< @@ -5590,18 +5582,19 @@ static int __pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__pyx_v_s * int tid, */ -static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser) { +static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser) { int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; int __pyx_t_3; + tabix_t *__pyx_t_4; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "ctabix.pyx":523 + /* "pysam/ctabix.pyx":523 * Parser parser ): * * assert tabixfile._isOpen() # <<<<<<<<<<<<<< @@ -5622,7 +5615,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct } #endif - /* "ctabix.pyx":524 + /* "pysam/ctabix.pyx":524 * * assert tabixfile._isOpen() * self.parser = parser # <<<<<<<<<<<<<< @@ -5635,16 +5628,17 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct __Pyx_DECREF(((PyObject *)__pyx_v_self->parser)); __pyx_v_self->parser = __pyx_v_parser; - /* "ctabix.pyx":528 + /* "pysam/ctabix.pyx":528 * # makes sure that samfile stays alive as long as the * # iterator is alive. * self.tabixfile = tabixfile.tabixfile # <<<<<<<<<<<<<< * * if tid < 0: */ - __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile; + __pyx_t_4 = __pyx_v_tabixfile->tabixfile; + __pyx_v_self->tabixfile = __pyx_t_4; - /* "ctabix.pyx":530 + /* "pysam/ctabix.pyx":530 * self.tabixfile = tabixfile.tabixfile * * if tid < 0: # <<<<<<<<<<<<<< @@ -5654,7 +5648,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct __pyx_t_3 = (__pyx_v_tid < 0); if (__pyx_t_3) { - /* "ctabix.pyx":533 + /* "pysam/ctabix.pyx":533 * # seek to start of file to ensure iteration is over * # all entries. * bgzf_seek( self.tabixfile.fp, 0, 0) # <<<<<<<<<<<<<< @@ -5663,7 +5657,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct */ bgzf_seek(__pyx_v_self->tabixfile->fp, 0, 0); - /* "ctabix.pyx":534 + /* "pysam/ctabix.pyx":534 * # all entries. * bgzf_seek( self.tabixfile.fp, 0, 0) * self.iterator = ti_iter_first() # <<<<<<<<<<<<<< @@ -5675,7 +5669,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct } /*else*/ { - /* "ctabix.pyx":536 + /* "pysam/ctabix.pyx":536 * self.iterator = ti_iter_first() * else: * self.iterator = ti_queryi(self.tabixfile, tid, start, end) # <<<<<<<<<<<<<< @@ -5686,7 +5680,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct } __pyx_L3:; - /* "ctabix.pyx":538 + /* "pysam/ctabix.pyx":538 * self.iterator = ti_queryi(self.tabixfile, tid, start, end) * * if self.iterator == NULL: # <<<<<<<<<<<<<< @@ -5696,7 +5690,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct __pyx_t_3 = (((void *)__pyx_v_self->iterator) == NULL); if (__pyx_t_3) { - /* "ctabix.pyx":539 + /* "pysam/ctabix.pyx":539 * * if self.iterator == NULL: * raise ValueError("malformatted query or wrong sequence name.\n") # <<<<<<<<<<<<<< @@ -5717,7 +5711,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.TabixIteratorParsed.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixIteratorParsed.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -5725,17 +5719,17 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_19TabixIteratorParsed_3__iter__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_19TabixIteratorParsed_3__iter__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_19TabixIteratorParsed_2__iter__(((struct __pyx_obj_6ctabix_TabixIteratorParsed *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":541 +/* "pysam/ctabix.pyx":541 * raise ValueError("malformatted query or wrong sequence name.\n") * * def __iter__(self): # <<<<<<<<<<<<<< @@ -5743,12 +5737,12 @@ static PyObject *__pyx_pw_6ctabix_19TabixIteratorParsed_3__iter__(PyObject *__py * */ -static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__", 0); - /* "ctabix.pyx":542 + /* "pysam/ctabix.pyx":542 * * def __iter__(self): * return self # <<<<<<<<<<<<<< @@ -5768,19 +5762,21 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_o } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_6ctabix_19TabixIteratorParsed_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; -struct wrapperbase __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__; -static PyObject *__pyx_pw_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; +#if CYTHON_COMPILING_IN_CPYTHON +struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__; +#endif +static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(((struct __pyx_obj_6ctabix_TabixIteratorParsed *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__(((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":544 +/* "pysam/ctabix.pyx":544 * return self * * def __next__(self): # <<<<<<<<<<<<<< @@ -5788,7 +5784,7 @@ static PyObject *__pyx_pw_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__py * */ -static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self) { char *__pyx_v_s; int __pyx_v_len; PyObject *__pyx_r = NULL; @@ -5802,7 +5798,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_o int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "ctabix.pyx":552 + /* "pysam/ctabix.pyx":552 * cdef char * s * cdef int len * while 1: # <<<<<<<<<<<<<< @@ -5812,7 +5808,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_o while (1) { if (!1) break; - /* "ctabix.pyx":553 + /* "pysam/ctabix.pyx":553 * cdef int len * while 1: * s = ti_read(self.tabixfile, self.iterator, &len) # <<<<<<<<<<<<<< @@ -5821,7 +5817,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_o */ __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); - /* "ctabix.pyx":554 + /* "pysam/ctabix.pyx":554 * while 1: * s = ti_read(self.tabixfile, self.iterator, &len) * if s == NULL: raise StopIteration # <<<<<<<<<<<<<< @@ -5836,7 +5832,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_o } __pyx_L5:; - /* "ctabix.pyx":556 + /* "pysam/ctabix.pyx":556 * if s == NULL: raise StopIteration * # todo: read metachar from configuration * if s[0] != '#': break # <<<<<<<<<<<<<< @@ -5852,7 +5848,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_o } __pyx_L4_break:; - /* "ctabix.pyx":558 + /* "pysam/ctabix.pyx":558 * if s[0] != '#': break * * return self.parser(s, len) # <<<<<<<<<<<<<< @@ -5885,7 +5881,7 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_o __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); - __Pyx_AddTraceback("ctabix.TabixIteratorParsed.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.TabixIteratorParsed.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -5894,15 +5890,15 @@ static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_o } /* Python wrapper */ -static void __pyx_pw_6ctabix_19TabixIteratorParsed_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_6ctabix_19TabixIteratorParsed_7__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_7__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_6ctabix_19TabixIteratorParsed_6__dealloc__(((struct __pyx_obj_6ctabix_TabixIteratorParsed *)__pyx_v_self)); + __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_6__dealloc__(((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } -/* "ctabix.pyx":560 +/* "pysam/ctabix.pyx":560 * return self.parser(s, len) * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -5910,12 +5906,12 @@ static void __pyx_pw_6ctabix_19TabixIteratorParsed_7__dealloc__(PyObject *__pyx_ * ti_iter_destroy(self.iterator) */ -static void __pyx_pf_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self) { +static void __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self) { __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_RefNannySetupContext("__dealloc__", 0); - /* "ctabix.pyx":561 + /* "pysam/ctabix.pyx":561 * * def __dealloc__(self): * if self.iterator != NULL: # <<<<<<<<<<<<<< @@ -5925,7 +5921,7 @@ static void __pyx_pf_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj __pyx_t_1 = (((void *)__pyx_v_self->iterator) != NULL); if (__pyx_t_1) { - /* "ctabix.pyx":562 + /* "pysam/ctabix.pyx":562 * def __dealloc__(self): * if self.iterator != NULL: * ti_iter_destroy(self.iterator) # <<<<<<<<<<<<<< @@ -5941,19 +5937,18 @@ static void __pyx_pf_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_1tabix_compress(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_6ctabix_tabix_compress[] = "tabix_compress(filename_in, filename_out, force=False)\n\n compress *filename_in* writing the output to *filename_out*.\n \n Raise an IOError if *filename_out* already exists, unless *force* is set.\n "; -static PyMethodDef __pyx_mdef_6ctabix_1tabix_compress = {__Pyx_NAMESTR("tabix_compress"), (PyCFunction)__pyx_pw_6ctabix_1tabix_compress, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_tabix_compress)}; -static PyObject *__pyx_pw_6ctabix_1tabix_compress(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_1tabix_compress(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_tabix_compress[] = "tabix_compress(filename_in, filename_out, force=False)\n\n compress *filename_in* writing the output to *filename_out*.\n \n Raise an IOError if *filename_out* already exists, unless *force* is set.\n "; +static PyMethodDef __pyx_mdef_5pysam_6ctabix_1tabix_compress = {__Pyx_NAMESTR("tabix_compress"), (PyCFunction)__pyx_pw_5pysam_6ctabix_1tabix_compress, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_tabix_compress)}; +static PyObject *__pyx_pw_5pysam_6ctabix_1tabix_compress(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_filename_in = 0; PyObject *__pyx_v_filename_out = 0; PyObject *__pyx_v_force = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename_in,&__pyx_n_s__filename_out,&__pyx_n_s__force,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("tabix_compress (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename_in,&__pyx_n_s__filename_out,&__pyx_n_s__force,0}; PyObject* values[3] = {0,0,0}; values[2] = __pyx_k_30; if (unlikely(__pyx_kwds)) { @@ -5969,12 +5964,10 @@ static PyObject *__pyx_pw_6ctabix_1tabix_compress(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_in); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_in)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_out); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_out)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("tabix_compress", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -6004,16 +5997,16 @@ static PyObject *__pyx_pw_6ctabix_1tabix_compress(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("tabix_compress", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_tabix_compress(__pyx_self, __pyx_v_filename_in, __pyx_v_filename_out, __pyx_v_force); + __pyx_r = __pyx_pf_5pysam_6ctabix_tabix_compress(__pyx_self, __pyx_v_filename_in, __pyx_v_filename_out, __pyx_v_force); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":564 +/* "pysam/ctabix.pyx":564 * ti_iter_destroy(self.iterator) * * def tabix_compress( filename_in, # <<<<<<<<<<<<<< @@ -6021,7 +6014,7 @@ static PyObject *__pyx_pw_6ctabix_1tabix_compress(PyObject *__pyx_self, PyObject * force = False ): */ -static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force) { +static PyObject *__pyx_pf_5pysam_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force) { int __pyx_v_WINDOW_SIZE; int __pyx_v_c; int __pyx_v_r; @@ -6045,7 +6038,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("tabix_compress", 0); - /* "ctabix.pyx":573 + /* "pysam/ctabix.pyx":573 * ''' * * if not force and os.path.exists(filename_out ): # <<<<<<<<<<<<<< @@ -6080,7 +6073,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s } if (__pyx_t_6) { - /* "ctabix.pyx":574 + /* "pysam/ctabix.pyx":574 * * if not force and os.path.exists(filename_out ): * raise IOError( "Filename '%s' already exists, use *force* to overwrite" % filename_out) # <<<<<<<<<<<<<< @@ -6104,7 +6097,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s } __pyx_L3:; - /* "ctabix.pyx":583 + /* "pysam/ctabix.pyx":583 * * cdef int O_RDONLY * O_RDONLY = os.O_RDONLY # <<<<<<<<<<<<<< @@ -6120,7 +6113,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_v_O_RDONLY = __pyx_t_7; - /* "ctabix.pyx":585 + /* "pysam/ctabix.pyx":585 * O_RDONLY = os.O_RDONLY * * WINDOW_SIZE = 64 * 1024 # <<<<<<<<<<<<<< @@ -6129,19 +6122,19 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_v_WINDOW_SIZE = 65536; - /* "ctabix.pyx":587 + /* "pysam/ctabix.pyx":587 * WINDOW_SIZE = 64 * 1024 * * fn = _force_bytes(filename_out) # <<<<<<<<<<<<<< * fp = bgzf_open( fn, "w") * if fp == NULL: */ - __pyx_t_4 = ((PyObject *)__pyx_f_6ctabix__force_bytes(__pyx_v_filename_out)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = ((PyObject *)__pyx_f_5pysam_6ctabix__force_bytes(__pyx_v_filename_out)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_v_fn = ((PyObject*)__pyx_t_4); __pyx_t_4 = 0; - /* "ctabix.pyx":588 + /* "pysam/ctabix.pyx":588 * * fn = _force_bytes(filename_out) * fp = bgzf_open( fn, "w") # <<<<<<<<<<<<<< @@ -6151,7 +6144,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __pyx_t_8 = PyBytes_AsString(((PyObject *)__pyx_v_fn)); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_fp = bgzf_open(__pyx_t_8, __pyx_k__w); - /* "ctabix.pyx":589 + /* "pysam/ctabix.pyx":589 * fn = _force_bytes(filename_out) * fp = bgzf_open( fn, "w") * if fp == NULL: # <<<<<<<<<<<<<< @@ -6161,7 +6154,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __pyx_t_6 = (__pyx_v_fp == NULL); if (__pyx_t_6) { - /* "ctabix.pyx":590 + /* "pysam/ctabix.pyx":590 * fp = bgzf_open( fn, "w") * if fp == NULL: * raise IOError( "could not open '%s' for writing" ) # <<<<<<<<<<<<<< @@ -6177,20 +6170,20 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s } __pyx_L4:; - /* "ctabix.pyx":592 + /* "pysam/ctabix.pyx":592 * raise IOError( "could not open '%s' for writing" ) * * fn = _force_bytes(filename_in) # <<<<<<<<<<<<<< * fd_src = open(fn, O_RDONLY) * if fd_src == 0: */ - __pyx_t_4 = ((PyObject *)__pyx_f_6ctabix__force_bytes(__pyx_v_filename_in)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = ((PyObject *)__pyx_f_5pysam_6ctabix__force_bytes(__pyx_v_filename_in)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(((PyObject *)__pyx_v_fn)); __pyx_v_fn = ((PyObject*)__pyx_t_4); __pyx_t_4 = 0; - /* "ctabix.pyx":593 + /* "pysam/ctabix.pyx":593 * * fn = _force_bytes(filename_in) * fd_src = open(fn, O_RDONLY) # <<<<<<<<<<<<<< @@ -6200,7 +6193,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __pyx_t_8 = PyBytes_AsString(((PyObject *)__pyx_v_fn)); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_fd_src = open(__pyx_t_8, __pyx_v_O_RDONLY); - /* "ctabix.pyx":594 + /* "pysam/ctabix.pyx":594 * fn = _force_bytes(filename_in) * fd_src = open(fn, O_RDONLY) * if fd_src == 0: # <<<<<<<<<<<<<< @@ -6210,7 +6203,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __pyx_t_6 = (__pyx_v_fd_src == 0); if (__pyx_t_6) { - /* "ctabix.pyx":595 + /* "pysam/ctabix.pyx":595 * fd_src = open(fn, O_RDONLY) * if fd_src == 0: * raise IOError( "could not open '%s' for reading" ) # <<<<<<<<<<<<<< @@ -6226,7 +6219,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s } __pyx_L5:; - /* "ctabix.pyx":597 + /* "pysam/ctabix.pyx":597 * raise IOError( "could not open '%s' for reading" ) * * buffer = malloc(WINDOW_SIZE) # <<<<<<<<<<<<<< @@ -6235,7 +6228,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_v_buffer = malloc(__pyx_v_WINDOW_SIZE); - /* "ctabix.pyx":598 + /* "pysam/ctabix.pyx":598 * * buffer = malloc(WINDOW_SIZE) * c = 1 # <<<<<<<<<<<<<< @@ -6244,7 +6237,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_v_c = 1; - /* "ctabix.pyx":600 + /* "pysam/ctabix.pyx":600 * c = 1 * * while c > 0: # <<<<<<<<<<<<<< @@ -6255,7 +6248,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __pyx_t_6 = (__pyx_v_c > 0); if (!__pyx_t_6) break; - /* "ctabix.pyx":601 + /* "pysam/ctabix.pyx":601 * * while c > 0: * c = read(fd_src, buffer, WINDOW_SIZE) # <<<<<<<<<<<<<< @@ -6264,7 +6257,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_v_c = read(__pyx_v_fd_src, __pyx_v_buffer, __pyx_v_WINDOW_SIZE); - /* "ctabix.pyx":602 + /* "pysam/ctabix.pyx":602 * while c > 0: * c = read(fd_src, buffer, WINDOW_SIZE) * r = bgzf_write(fp, buffer, c) # <<<<<<<<<<<<<< @@ -6273,7 +6266,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_v_r = bgzf_write(__pyx_v_fp, __pyx_v_buffer, __pyx_v_c); - /* "ctabix.pyx":603 + /* "pysam/ctabix.pyx":603 * c = read(fd_src, buffer, WINDOW_SIZE) * r = bgzf_write(fp, buffer, c) * if r < 0: # <<<<<<<<<<<<<< @@ -6283,7 +6276,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __pyx_t_6 = (__pyx_v_r < 0); if (__pyx_t_6) { - /* "ctabix.pyx":604 + /* "pysam/ctabix.pyx":604 * r = bgzf_write(fp, buffer, c) * if r < 0: * free( buffer ) # <<<<<<<<<<<<<< @@ -6292,7 +6285,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ free(__pyx_v_buffer); - /* "ctabix.pyx":605 + /* "pysam/ctabix.pyx":605 * if r < 0: * free( buffer ) * raise OSError("writing failed") # <<<<<<<<<<<<<< @@ -6309,7 +6302,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __pyx_L8:; } - /* "ctabix.pyx":607 + /* "pysam/ctabix.pyx":607 * raise OSError("writing failed") * * free( buffer ) # <<<<<<<<<<<<<< @@ -6318,7 +6311,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ free(__pyx_v_buffer); - /* "ctabix.pyx":608 + /* "pysam/ctabix.pyx":608 * * free( buffer ) * r = bgzf_close(fp) # <<<<<<<<<<<<<< @@ -6327,7 +6320,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_v_r = bgzf_close(__pyx_v_fp); - /* "ctabix.pyx":609 + /* "pysam/ctabix.pyx":609 * free( buffer ) * r = bgzf_close(fp) * if r < 0: raise OSError("writing failed") # <<<<<<<<<<<<<< @@ -6351,7 +6344,7 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); - __Pyx_AddTraceback("ctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_compress", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_fn); @@ -6361,10 +6354,10 @@ static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_6ctabix_2tabix_index[] = "tabix_index(filename, force=False, seq_col=None, start_col=None, end_col=None, preset=None, meta_char='#', zerobased=False)\n\n index tab-separated *filename* using tabix.\n\n An existing index will not be overwritten unless\n *force* is set.\n\n The index will be built from coordinates\n in columns *seq_col*, *start_col* and *end_col*.\n\n The contents of *filename* have to be sorted by \n contig and position - the method does not check\n if the file is sorted.\n\n Column indices are 0-based. Coordinates in the file\n are assumed to be 1-based.\n\n If *preset* is provided, the column coordinates\n are taken from a preset. Valid values for preset\n are \"gff\", \"bed\", \"sam\", \"vcf\", psltbl\", \"pileup\".\n \n Lines beginning with *meta_char* and the first\n *line_skip* lines will be skipped.\n \n If *filename* does not end in \".gz\", it will be automatically\n compressed. The original file will be removed and only the \n compressed file will be retained. \n\n If *filename* ends in *gz*, the file is assumed to be already\n compressed with bgzf.\n\n returns the filename of the compressed data\n "; -static PyMethodDef __pyx_mdef_6ctabix_3tabix_index = {__Pyx_NAMESTR("tabix_index"), (PyCFunction)__pyx_pw_6ctabix_3tabix_index, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_2tabix_index)}; -static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_2tabix_index[] = "tabix_index(filename, force=False, seq_col=None, start_col=None, end_col=None, preset=None, meta_char='#', zerobased=False)\n\n index tab-separated *filename* using tabix.\n\n An existing index will not be overwritten unless\n *force* is set.\n\n The index will be built from coordinates\n in columns *seq_col*, *start_col* and *end_col*.\n\n The contents of *filename* have to be sorted by \n contig and position - the method does not check\n if the file is sorted.\n\n Column indices are 0-based. Coordinates in the file\n are assumed to be 1-based.\n\n If *preset* is provided, the column coordinates\n are taken from a preset. Valid values for preset\n are \"gff\", \"bed\", \"sam\", \"vcf\", psltbl\", \"pileup\".\n \n Lines beginning with *meta_char* and the first\n *line_skip* lines will be skipped.\n \n If *filename* does not end in \".gz\", it will be automatically\n compressed. The original file will be removed and only the \n compressed file will be retained. \n\n If *filename* ends in *gz*, the file is assumed to be already\n compressed with bgzf.\n\n returns the filename of the compressed data\n "; +static PyMethodDef __pyx_mdef_5pysam_6ctabix_3tabix_index = {__Pyx_NAMESTR("tabix_index"), (PyCFunction)__pyx_pw_5pysam_6ctabix_3tabix_index, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_2tabix_index)}; +static PyObject *__pyx_pw_5pysam_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_filename = 0; PyObject *__pyx_v_force = 0; PyObject *__pyx_v_seq_col = 0; @@ -6373,16 +6366,15 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_ PyObject *__pyx_v_preset = 0; PyObject *__pyx_v_meta_char = 0; PyObject *__pyx_v_zerobased = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__force,&__pyx_n_s__seq_col,&__pyx_n_s__start_col,&__pyx_n_s__end_col,&__pyx_n_s__preset,&__pyx_n_s__meta_char,&__pyx_n_s__zerobased,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("tabix_index (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__force,&__pyx_n_s__seq_col,&__pyx_n_s__start_col,&__pyx_n_s__end_col,&__pyx_n_s__preset,&__pyx_n_s__meta_char,&__pyx_n_s__zerobased,0}; PyObject* values[8] = {0,0,0,0,0,0,0,0}; values[1] = __pyx_k_39; - /* "ctabix.pyx":613 + /* "pysam/ctabix.pyx":613 * def tabix_index( filename, * force = False, * seq_col = None, # <<<<<<<<<<<<<< @@ -6391,7 +6383,7 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_ */ values[2] = ((PyObject *)Py_None); - /* "ctabix.pyx":614 + /* "pysam/ctabix.pyx":614 * force = False, * seq_col = None, * start_col = None, # <<<<<<<<<<<<<< @@ -6400,7 +6392,7 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_ */ values[3] = ((PyObject *)Py_None); - /* "ctabix.pyx":615 + /* "pysam/ctabix.pyx":615 * seq_col = None, * start_col = None, * end_col = None, # <<<<<<<<<<<<<< @@ -6409,7 +6401,7 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_ */ values[4] = ((PyObject *)Py_None); - /* "ctabix.pyx":616 + /* "pysam/ctabix.pyx":616 * start_col = None, * end_col = None, * preset = None, # <<<<<<<<<<<<<< @@ -6437,8 +6429,7 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (kw_args > 0) { @@ -6506,16 +6497,16 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("tabix_index", 0, 1, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_2tabix_index(__pyx_self, __pyx_v_filename, __pyx_v_force, __pyx_v_seq_col, __pyx_v_start_col, __pyx_v_end_col, __pyx_v_preset, __pyx_v_meta_char, __pyx_v_zerobased); + __pyx_r = __pyx_pf_5pysam_6ctabix_2tabix_index(__pyx_self, __pyx_v_filename, __pyx_v_force, __pyx_v_seq_col, __pyx_v_start_col, __pyx_v_end_col, __pyx_v_preset, __pyx_v_meta_char, __pyx_v_zerobased); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":611 +/* "pysam/ctabix.pyx":611 * if r < 0: raise OSError("writing failed") * * def tabix_index( filename, # <<<<<<<<<<<<<< @@ -6523,7 +6514,7 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_ * seq_col = None, */ -static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased) { +static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased) { PyObject *__pyx_v_preset2conf = NULL; PyObject *__pyx_v_conf_data = NULL; ti_conf_t __pyx_v_conf; @@ -6562,7 +6553,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_INCREF(__pyx_v_end_col); __Pyx_INCREF(__pyx_v_preset); - /* "ctabix.pyx":653 + /* "pysam/ctabix.pyx":653 * ''' * * if not os.path.exists(filename): raise IOError("No such file '%s'" % filename) # <<<<<<<<<<<<<< @@ -6607,30 +6598,26 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L3:; - /* "ctabix.pyx":655 + /* "pysam/ctabix.pyx":655 * if not os.path.exists(filename): raise IOError("No such file '%s'" % filename) * * if preset == None and (seq_col == None or start_col == None or end_col == None): # <<<<<<<<<<<<<< * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) * */ - __pyx_t_3 = PyObject_RichCompare(__pyx_v_preset, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_preset, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_5) { - __pyx_t_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (!__pyx_t_4) { - __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (!__pyx_t_6) { - __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_8 = __pyx_t_7; @@ -6647,7 +6634,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } if (__pyx_t_4) { - /* "ctabix.pyx":656 + /* "pysam/ctabix.pyx":656 * * if preset == None and (seq_col == None or start_col == None or end_col == None): * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) # <<<<<<<<<<<<<< @@ -6663,7 +6650,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L4:; - /* "ctabix.pyx":658 + /* "pysam/ctabix.pyx":658 * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) * * if not filename.endswith(".gz"): # <<<<<<<<<<<<<< @@ -6680,7 +6667,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __pyx_t_5 = (!__pyx_t_4); if (__pyx_t_5) { - /* "ctabix.pyx":659 + /* "pysam/ctabix.pyx":659 * * if not filename.endswith(".gz"): * tabix_compress( filename, filename + ".gz", force = force ) # <<<<<<<<<<<<<< @@ -6709,7 +6696,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "ctabix.pyx":660 + /* "pysam/ctabix.pyx":660 * if not filename.endswith(".gz"): * tabix_compress( filename, filename + ".gz", force = force ) * os.unlink( filename ) # <<<<<<<<<<<<<< @@ -6732,7 +6719,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":661 + /* "pysam/ctabix.pyx":661 * tabix_compress( filename, filename + ".gz", force = force ) * os.unlink( filename ) * filename += ".gz" # <<<<<<<<<<<<<< @@ -6748,7 +6735,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L5:; - /* "ctabix.pyx":663 + /* "pysam/ctabix.pyx":663 * filename += ".gz" * * if not force and os.path.exists(filename + ".tbi" ): # <<<<<<<<<<<<<< @@ -6785,7 +6772,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } if (__pyx_t_6) { - /* "ctabix.pyx":664 + /* "pysam/ctabix.pyx":664 * * if not force and os.path.exists(filename + ".tbi" ): * raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" ) # <<<<<<<<<<<<<< @@ -6801,7 +6788,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L6:; - /* "ctabix.pyx":669 + /* "pysam/ctabix.pyx":669 * # preset-code, contig, start, end, metachar for commends, lines to ignore at beginning * # 0 is a missing column * preset2conf = { # <<<<<<<<<<<<<< @@ -6811,7 +6798,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_9)); - /* "ctabix.pyx":670 + /* "pysam/ctabix.pyx":670 * # 0 is a missing column * preset2conf = { * 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), # <<<<<<<<<<<<<< @@ -6841,7 +6828,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__gff), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":671 + /* "pysam/ctabix.pyx":671 * preset2conf = { * 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), # <<<<<<<<<<<<<< @@ -6871,7 +6858,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__bed), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":672 + /* "pysam/ctabix.pyx":672 * 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), * 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), # <<<<<<<<<<<<<< @@ -6901,7 +6888,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__psltbl), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":673 + /* "pysam/ctabix.pyx":673 * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), * 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), * 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ), # <<<<<<<<<<<<<< @@ -6931,7 +6918,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__sam), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":674 + /* "pysam/ctabix.pyx":674 * 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), * 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ), * 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ), # <<<<<<<<<<<<<< @@ -6961,7 +6948,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__vcf), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":675 + /* "pysam/ctabix.pyx":675 * 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ), * 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ), * 'pileup': (3, 1, 2, 0, ord('#'), 0 ), # <<<<<<<<<<<<<< @@ -6993,7 +6980,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __pyx_v_preset2conf = __pyx_t_9; __pyx_t_9 = 0; - /* "ctabix.pyx":678 + /* "pysam/ctabix.pyx":678 * } * * if preset: # <<<<<<<<<<<<<< @@ -7003,7 +6990,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_preset); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_6) { - /* "ctabix.pyx":679 + /* "pysam/ctabix.pyx":679 * * if preset: * try: # <<<<<<<<<<<<<< @@ -7017,7 +7004,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_XGOTREF(__pyx_t_12); /*try:*/ { - /* "ctabix.pyx":680 + /* "pysam/ctabix.pyx":680 * if preset: * try: * conf_data = preset2conf[preset] # <<<<<<<<<<<<<< @@ -7039,7 +7026,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "ctabix.pyx":681 + /* "pysam/ctabix.pyx":681 * try: * conf_data = preset2conf[preset] * except KeyError: # <<<<<<<<<<<<<< @@ -7048,13 +7035,13 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel */ __pyx_t_13 = PyErr_ExceptionMatches(__pyx_builtin_KeyError); if (__pyx_t_13) { - __Pyx_AddTraceback("ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_3, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_GOTREF(__pyx_t_3); __Pyx_GOTREF(__pyx_t_1); - /* "ctabix.pyx":682 + /* "pysam/ctabix.pyx":682 * conf_data = preset2conf[preset] * except KeyError: * raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys() ))) # <<<<<<<<<<<<<< @@ -7118,15 +7105,14 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } /*else*/ { - /* "ctabix.pyx":684 + /* "pysam/ctabix.pyx":684 * raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys() ))) * else: * if end_col == None: end_col = -1 # <<<<<<<<<<<<<< * preset = 0 * */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_6) { @@ -7137,7 +7123,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L18:; - /* "ctabix.pyx":685 + /* "pysam/ctabix.pyx":685 * else: * if end_col == None: end_col = -1 * preset = 0 # <<<<<<<<<<<<<< @@ -7148,7 +7134,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_DECREF(__pyx_v_preset); __pyx_v_preset = __pyx_int_0; - /* "ctabix.pyx":692 + /* "pysam/ctabix.pyx":692 * # -1 is subtracted from the start coordinate. To avoid doing this, set * # the TI_FLAG_UCSC=0x10000 flag: * if zerobased: preset = preset | 0x10000 # <<<<<<<<<<<<<< @@ -7166,7 +7152,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L19:; - /* "ctabix.pyx":694 + /* "pysam/ctabix.pyx":694 * if zerobased: preset = preset | 0x10000 * * conf_data = (preset, seq_col+1, start_col+1, end_col+1, ord(meta_char), 0) # <<<<<<<<<<<<<< @@ -7212,7 +7198,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L7:; - /* "ctabix.pyx":697 + /* "pysam/ctabix.pyx":697 * * cdef ti_conf_t conf * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data # <<<<<<<<<<<<<< @@ -7221,12 +7207,18 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel */ if ((likely(PyTuple_CheckExact(__pyx_v_conf_data))) || (PyList_CheckExact(__pyx_v_conf_data))) { PyObject* sequence = __pyx_v_conf_data; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 6)) { + if (size > 6) __Pyx_RaiseTooManyValuesError(6); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 6)) { - if (PyTuple_GET_SIZE(sequence) > 6) __Pyx_RaiseTooManyValuesError(6); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_14 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_15 = PyTuple_GET_ITEM(sequence, 1); __pyx_t_9 = PyTuple_GET_ITEM(sequence, 2); @@ -7234,11 +7226,6 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __pyx_t_1 = PyTuple_GET_ITEM(sequence, 4); __pyx_t_2 = PyTuple_GET_ITEM(sequence, 5); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 6)) { - if (PyList_GET_SIZE(sequence) > 6) __Pyx_RaiseTooManyValuesError(6); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_14 = PyList_GET_ITEM(sequence, 0); __pyx_t_15 = PyList_GET_ITEM(sequence, 1); __pyx_t_9 = PyList_GET_ITEM(sequence, 2); @@ -7252,30 +7239,34 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_INCREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); __Pyx_INCREF(__pyx_t_2); - } else { + #else + Py_ssize_t i; + PyObject** temps[6] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_9,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2}; + for (i=0; i < 6; i++) { + PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + *(temps[i]) = item; + } + #endif + } else + { Py_ssize_t index = -1; - __pyx_t_16 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_16); - __pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext; - index = 0; __pyx_t_14 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_14)) goto __pyx_L20_unpacking_failed; - __Pyx_GOTREF(__pyx_t_14); - index = 1; __pyx_t_15 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_15)) goto __pyx_L20_unpacking_failed; - __Pyx_GOTREF(__pyx_t_15); - index = 2; __pyx_t_9 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_9)) goto __pyx_L20_unpacking_failed; - __Pyx_GOTREF(__pyx_t_9); - index = 3; __pyx_t_3 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_3)) goto __pyx_L20_unpacking_failed; - __Pyx_GOTREF(__pyx_t_3); - index = 4; __pyx_t_1 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_1)) goto __pyx_L20_unpacking_failed; - __Pyx_GOTREF(__pyx_t_1); - index = 5; __pyx_t_2 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_2)) goto __pyx_L20_unpacking_failed; - __Pyx_GOTREF(__pyx_t_2); + PyObject** temps[6] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_9,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2}; + __pyx_t_16 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_16); + __pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext; + for (index=0; index < 6; index++) { + PyObject* item = __pyx_t_17(__pyx_t_16); if (unlikely(!item)) goto __pyx_L20_unpacking_failed; + __Pyx_GOTREF(item); + *(temps[index]) = item; + } if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_16), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_17 = NULL; __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; goto __pyx_L21_unpacking_done; __pyx_L20_unpacking_failed:; __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_17 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L21_unpacking_done:; } @@ -7298,19 +7289,19 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __pyx_v_conf.meta_char = __pyx_t_22; __pyx_v_conf.line_skip = __pyx_t_23; - /* "ctabix.pyx":699 + /* "pysam/ctabix.pyx":699 * conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data * * fn = _my_encodeFilename( filename ) # <<<<<<<<<<<<<< * ti_index_build( fn, &conf) * */ - __pyx_t_2 = ((PyObject *)__pyx_f_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_v_fn = ((PyObject*)__pyx_t_2); __pyx_t_2 = 0; - /* "ctabix.pyx":700 + /* "pysam/ctabix.pyx":700 * * fn = _my_encodeFilename( filename ) * ti_index_build( fn, &conf) # <<<<<<<<<<<<<< @@ -7320,7 +7311,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __pyx_t_24 = PyBytes_AsString(((PyObject *)__pyx_v_fn)); if (unlikely((!__pyx_t_24) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ti_index_build(__pyx_t_24, (&__pyx_v_conf)); - /* "ctabix.pyx":702 + /* "pysam/ctabix.pyx":702 * ti_index_build( fn, &conf) * * return filename # <<<<<<<<<<<<<< @@ -7342,7 +7333,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_XDECREF(__pyx_t_14); __Pyx_XDECREF(__pyx_t_15); __Pyx_XDECREF(__pyx_t_16); - __Pyx_AddTraceback("ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_preset2conf); @@ -7357,15 +7348,15 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel } /* Python wrapper */ -static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_infile = 0; int __pyx_v_buffer_size; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__buffer_size,0}; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__buffer_size,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -7379,8 +7370,7 @@ static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (kw_args > 0) { @@ -7391,10 +7381,6 @@ static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_ if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } - if (values[1]) { - } else { - __pyx_v_buffer_size = ((int)65536); - } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); @@ -7414,16 +7400,16 @@ static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.tabix_inplace_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_inplace_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(((struct __pyx_obj_6ctabix_tabix_inplace_iterator *)__pyx_v_self), __pyx_v_infile, __pyx_v_buffer_size); + __pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator___cinit__(((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)__pyx_v_self), __pyx_v_infile, __pyx_v_buffer_size); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":719 +/* "pysam/ctabix.pyx":719 * * * def __cinit__(self, infile, int buffer_size = 65536 ): # <<<<<<<<<<<<<< @@ -7431,7 +7417,7 @@ static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_ * cdef int fd = PyObject_AsFileDescriptor( infile ) */ -static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size) { +static int __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size) { int __pyx_v_fd; int __pyx_r; __Pyx_RefNannyDeclarations @@ -7443,7 +7429,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "ctabix.pyx":721 + /* "pysam/ctabix.pyx":721 * def __cinit__(self, infile, int buffer_size = 65536 ): * * cdef int fd = PyObject_AsFileDescriptor( infile ) # <<<<<<<<<<<<<< @@ -7453,7 +7439,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ __pyx_t_1 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 721; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_fd = __pyx_t_1; - /* "ctabix.pyx":722 + /* "pysam/ctabix.pyx":722 * * cdef int fd = PyObject_AsFileDescriptor( infile ) * if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -7471,7 +7457,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ } __pyx_L3:; - /* "ctabix.pyx":723 + /* "pysam/ctabix.pyx":723 * cdef int fd = PyObject_AsFileDescriptor( infile ) * if fd == -1: raise ValueError( "I/O operation on closed file." ) * self.infile = fdopen( fd, 'r') # <<<<<<<<<<<<<< @@ -7480,7 +7466,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ */ __pyx_v_self->infile = fdopen(__pyx_v_fd, __pyx_k__r); - /* "ctabix.pyx":725 + /* "pysam/ctabix.pyx":725 * self.infile = fdopen( fd, 'r') * * if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -7498,7 +7484,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ } __pyx_L4:; - /* "ctabix.pyx":727 + /* "pysam/ctabix.pyx":727 * if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) * * self.buffer = malloc( buffer_size ) # <<<<<<<<<<<<<< @@ -7507,7 +7493,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ */ __pyx_v_self->buffer = ((char *)malloc(__pyx_v_buffer_size)); - /* "ctabix.pyx":728 + /* "pysam/ctabix.pyx":728 * * self.buffer = malloc( buffer_size ) * self.size = buffer_size # <<<<<<<<<<<<<< @@ -7520,7 +7506,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("ctabix.tabix_inplace_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_inplace_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -7528,17 +7514,17 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_ } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_3__iter__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_3__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(((struct __pyx_obj_6ctabix_tabix_inplace_iterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_2__iter__(((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":730 +/* "pysam/ctabix.pyx":730 * self.size = buffer_size * * def __iter__(self): # <<<<<<<<<<<<<< @@ -7546,12 +7532,12 @@ static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_3__iter__(PyObject *_ * */ -static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__", 0); - /* "ctabix.pyx":731 + /* "pysam/ctabix.pyx":731 * * def __iter__(self): * return self # <<<<<<<<<<<<<< @@ -7570,7 +7556,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __py return __pyx_r; } -/* "ctabix.pyx":733 +/* "pysam/ctabix.pyx":733 * return self * * cdef __cnext__(self): # <<<<<<<<<<<<<< @@ -7578,51 +7564,53 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __py * cdef char * b */ -static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self) { +static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self) { char *__pyx_v_b; size_t __pyx_v_nbytes; PyObject *__pyx_v_r = NULL; char *__pyx_v_result; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; + char *__pyx_t_1; PyObject *__pyx_t_2 = NULL; - int __pyx_t_3; + PyObject *__pyx_t_3 = NULL; int __pyx_t_4; int __pyx_t_5; int __pyx_t_6; - PyObject *__pyx_t_7 = NULL; + int __pyx_t_7; PyObject *__pyx_t_8 = NULL; + PyObject *__pyx_t_9 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cnext__", 0); - /* "ctabix.pyx":737 + /* "pysam/ctabix.pyx":737 * cdef char * b * cdef size_t nbytes * b = self.buffer # <<<<<<<<<<<<<< * r = self.Parser() * */ - __pyx_v_b = __pyx_v_self->buffer; + __pyx_t_1 = __pyx_v_self->buffer; + __pyx_v_b = __pyx_t_1; - /* "ctabix.pyx":738 + /* "pysam/ctabix.pyx":738 * cdef size_t nbytes * b = self.buffer * r = self.Parser() # <<<<<<<<<<<<<< * * while not feof( self.infile ): */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_v_r = __pyx_t_2; - __pyx_t_2 = 0; + __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_r = __pyx_t_3; + __pyx_t_3 = 0; - /* "ctabix.pyx":740 + /* "pysam/ctabix.pyx":740 * r = self.Parser() * * while not feof( self.infile ): # <<<<<<<<<<<<<< @@ -7630,10 +7618,10 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx * */ while (1) { - __pyx_t_3 = (!feof(__pyx_v_self->infile)); - if (!__pyx_t_3) break; + __pyx_t_4 = (!feof(__pyx_v_self->infile)); + if (!__pyx_t_4) break; - /* "ctabix.pyx":741 + /* "pysam/ctabix.pyx":741 * * while not feof( self.infile ): * nbytes = getline( &b, &self.size, self.infile) # <<<<<<<<<<<<<< @@ -7642,77 +7630,77 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx */ __pyx_v_nbytes = getline((&__pyx_v_b), (&__pyx_v_self->size), __pyx_v_self->infile); - /* "ctabix.pyx":744 + /* "pysam/ctabix.pyx":744 * * # stop at first error or eof * if (nbytes == -1): break # <<<<<<<<<<<<<< * # skip comments * if (b[0] == '#'): continue */ - __pyx_t_3 = (__pyx_v_nbytes == -1); - if (__pyx_t_3) { + __pyx_t_4 = (__pyx_v_nbytes == -1); + if (__pyx_t_4) { goto __pyx_L4_break; goto __pyx_L5; } __pyx_L5:; - /* "ctabix.pyx":746 + /* "pysam/ctabix.pyx":746 * if (nbytes == -1): break * # skip comments * if (b[0] == '#'): continue # <<<<<<<<<<<<<< * * # skip empty lines */ - __pyx_t_3 = ((__pyx_v_b[0]) == '#'); - if (__pyx_t_3) { + __pyx_t_4 = ((__pyx_v_b[0]) == '#'); + if (__pyx_t_4) { goto __pyx_L3_continue; goto __pyx_L6; } __pyx_L6:; - /* "ctabix.pyx":749 + /* "pysam/ctabix.pyx":749 * * # skip empty lines * if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # <<<<<<<<<<<<<< * * # make sure that entry is complete */ - __pyx_t_3 = ((__pyx_v_b[0]) == '\x00'); - if (!__pyx_t_3) { - __pyx_t_4 = ((__pyx_v_b[0]) == '\n'); - if (!__pyx_t_4) { - __pyx_t_5 = ((__pyx_v_b[0]) == '\r'); - __pyx_t_6 = __pyx_t_5; + __pyx_t_4 = ((__pyx_v_b[0]) == '\x00'); + if (!__pyx_t_4) { + __pyx_t_5 = ((__pyx_v_b[0]) == '\n'); + if (!__pyx_t_5) { + __pyx_t_6 = ((__pyx_v_b[0]) == '\r'); + __pyx_t_7 = __pyx_t_6; } else { - __pyx_t_6 = __pyx_t_4; + __pyx_t_7 = __pyx_t_5; } - __pyx_t_4 = __pyx_t_6; + __pyx_t_5 = __pyx_t_7; } else { - __pyx_t_4 = __pyx_t_3; + __pyx_t_5 = __pyx_t_4; } - if (__pyx_t_4) { + if (__pyx_t_5) { goto __pyx_L3_continue; goto __pyx_L7; } __pyx_L7:; - /* "ctabix.pyx":752 + /* "pysam/ctabix.pyx":752 * * # make sure that entry is complete * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # <<<<<<<<<<<<<< * result = b * raise ValueError( "incomplete line at %s" % result ) */ - __pyx_t_4 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n'); - if (__pyx_t_4) { - __pyx_t_3 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r'); - __pyx_t_6 = __pyx_t_3; + __pyx_t_5 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n'); + if (__pyx_t_5) { + __pyx_t_4 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r'); + __pyx_t_7 = __pyx_t_4; } else { - __pyx_t_6 = __pyx_t_4; + __pyx_t_7 = __pyx_t_5; } - if (__pyx_t_6) { + if (__pyx_t_7) { - /* "ctabix.pyx":753 + /* "pysam/ctabix.pyx":753 * # make sure that entry is complete * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': * result = b # <<<<<<<<<<<<<< @@ -7721,61 +7709,61 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx */ __pyx_v_result = __pyx_v_b; - /* "ctabix.pyx":754 + /* "pysam/ctabix.pyx":754 * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': * result = b * raise ValueError( "incomplete line at %s" % result ) # <<<<<<<<<<<<<< * * # make sure that this goes fully through C */ - __pyx_t_2 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); - __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2)); + __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); - __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __Pyx_Raise(__pyx_t_1, 0, 0, 0); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_2, 0, 0, 0); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L8; } __pyx_L8:; - /* "ctabix.pyx":760 + /* "pysam/ctabix.pyx":760 * # Python object causing segfaults as * # the wrong memory is freed * r.present( b, nbytes ) # <<<<<<<<<<<<<< * return r * */ - __pyx_t_1 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__present); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_2)); - __pyx_t_7 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__present); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); + __pyx_t_8 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_2)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); - PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7); - __Pyx_GIVEREF(__pyx_t_7); - __pyx_t_2 = 0; - __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_3)); + __Pyx_GIVEREF(((PyObject *)__pyx_t_3)); + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8); + __Pyx_GIVEREF(__pyx_t_8); + __pyx_t_3 = 0; + __pyx_t_8 = 0; + __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "ctabix.pyx":761 + /* "pysam/ctabix.pyx":761 * # the wrong memory is freed * r.present( b, nbytes ) * return r # <<<<<<<<<<<<<< @@ -7790,7 +7778,7 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx } __pyx_L4_break:; - /* "ctabix.pyx":763 + /* "pysam/ctabix.pyx":763 * return r * * raise StopIteration # <<<<<<<<<<<<<< @@ -7803,11 +7791,11 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_XDECREF(__pyx_t_7); + __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_8); - __Pyx_AddTraceback("ctabix.tabix_inplace_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_AddTraceback("pysam.ctabix.tabix_inplace_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XDECREF(__pyx_v_r); @@ -7817,15 +7805,15 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx } /* Python wrapper */ -static void __pyx_pw_6ctabix_22tabix_inplace_iterator_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_6ctabix_22tabix_inplace_iterator_5__dealloc__(PyObject *__pyx_v_self) { +static void __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_5__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_6ctabix_22tabix_inplace_iterator_4__dealloc__(((struct __pyx_obj_6ctabix_tabix_inplace_iterator *)__pyx_v_self)); + __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_4__dealloc__(((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } -/* "ctabix.pyx":765 +/* "pysam/ctabix.pyx":765 * raise StopIteration * * def __dealloc__(self): # <<<<<<<<<<<<<< @@ -7833,11 +7821,11 @@ static void __pyx_pw_6ctabix_22tabix_inplace_iterator_5__dealloc__(PyObject *__p * */ -static void __pyx_pf_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self) { +static void __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__", 0); - /* "ctabix.pyx":766 + /* "pysam/ctabix.pyx":766 * * def __dealloc__(self): * free(self.buffer) # <<<<<<<<<<<<<< @@ -7850,17 +7838,17 @@ static void __pyx_pf_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_ } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(((struct __pyx_obj_6ctabix_tabix_inplace_iterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_6__next__(((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":768 +/* "pysam/ctabix.pyx":768 * free(self.buffer) * * def __next__(self): # <<<<<<<<<<<<<< @@ -7868,7 +7856,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__(PyObject *_ * */ -static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -7877,7 +7865,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __py int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "ctabix.pyx":769 + /* "pysam/ctabix.pyx":769 * * def __next__(self): * return self.__cnext__() # <<<<<<<<<<<<<< @@ -7885,7 +7873,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __py * ctypedef class tabix_copy_iterator: */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -7895,7 +7883,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __py goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.tabix_inplace_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_inplace_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -7904,15 +7892,15 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __py } /* Python wrapper */ -static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_infile = 0; - struct __pyx_obj_6ctabix_Parser *__pyx_v_parser = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0}; + struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -7926,12 +7914,10 @@ static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_s kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -7946,18 +7932,18 @@ static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_s values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_infile = values[0]; - __pyx_v_parser = ((struct __pyx_obj_6ctabix_Parser *)values[1]); + __pyx_v_parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)values[1]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.tabix_copy_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_copy_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_6ctabix_Parser, 1, "parser", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(((struct __pyx_obj_6ctabix_tabix_copy_iterator *)__pyx_v_self), __pyx_v_infile, __pyx_v_parser); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_5pysam_6ctabix_Parser, 1, "parser", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator___cinit__(((struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)__pyx_v_self), __pyx_v_infile, __pyx_v_parser); goto __pyx_L0; __pyx_L1_error:; __pyx_r = -1; @@ -7966,7 +7952,7 @@ static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_s return __pyx_r; } -/* "ctabix.pyx":780 +/* "pysam/ctabix.pyx":780 * ''' * * def __cinit__(self, infile, Parser parser ): # <<<<<<<<<<<<<< @@ -7974,7 +7960,7 @@ static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_s * cdef int fd = PyObject_AsFileDescriptor( infile ) */ -static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser) { +static int __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser) { int __pyx_v_fd; int __pyx_r; __Pyx_RefNannyDeclarations @@ -7986,7 +7972,7 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "ctabix.pyx":782 + /* "pysam/ctabix.pyx":782 * def __cinit__(self, infile, Parser parser ): * * cdef int fd = PyObject_AsFileDescriptor( infile ) # <<<<<<<<<<<<<< @@ -7996,7 +7982,7 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct __pyx_t_1 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_fd = __pyx_t_1; - /* "ctabix.pyx":783 + /* "pysam/ctabix.pyx":783 * * cdef int fd = PyObject_AsFileDescriptor( infile ) * if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -8014,7 +8000,7 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct } __pyx_L3:; - /* "ctabix.pyx":784 + /* "pysam/ctabix.pyx":784 * cdef int fd = PyObject_AsFileDescriptor( infile ) * if fd == -1: raise ValueError( "I/O operation on closed file." ) * self.infile = fdopen( fd, 'r') # <<<<<<<<<<<<<< @@ -8023,7 +8009,7 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct */ __pyx_v_self->infile = fdopen(__pyx_v_fd, __pyx_k__r); - /* "ctabix.pyx":785 + /* "pysam/ctabix.pyx":785 * if fd == -1: raise ValueError( "I/O operation on closed file." ) * self.infile = fdopen( fd, 'r') * if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -8041,7 +8027,7 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct } __pyx_L4:; - /* "ctabix.pyx":786 + /* "pysam/ctabix.pyx":786 * self.infile = fdopen( fd, 'r') * if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) * self.parser = parser # <<<<<<<<<<<<<< @@ -8058,7 +8044,7 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("ctabix.tabix_copy_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_copy_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -8066,17 +8052,17 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_3__iter__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_3__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_3__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(((struct __pyx_obj_6ctabix_tabix_copy_iterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_2__iter__(((struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":788 +/* "pysam/ctabix.pyx":788 * self.parser = parser * * def __iter__(self): # <<<<<<<<<<<<<< @@ -8084,12 +8070,12 @@ static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_3__iter__(PyObject *__py * */ -static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__", 0); - /* "ctabix.pyx":789 + /* "pysam/ctabix.pyx":789 * * def __iter__(self): * return self # <<<<<<<<<<<<<< @@ -8108,7 +8094,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_o return __pyx_r; } -/* "ctabix.pyx":791 +/* "pysam/ctabix.pyx":791 * return self * * cdef __cnext__(self): # <<<<<<<<<<<<<< @@ -8116,7 +8102,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_o * cdef char * b */ -static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self) { +static PyObject *__pyx_f_5pysam_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self) { char *__pyx_v_b; size_t __pyx_v_nbytes; char *__pyx_v_result; @@ -8134,7 +8120,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cnext__", 0); - /* "ctabix.pyx":797 + /* "pysam/ctabix.pyx":797 * cdef int x * * b = NULL # <<<<<<<<<<<<<< @@ -8143,7 +8129,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob */ __pyx_v_b = NULL; - /* "ctabix.pyx":799 + /* "pysam/ctabix.pyx":799 * b = NULL * * while not feof( self.infile ): # <<<<<<<<<<<<<< @@ -8154,7 +8140,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob __pyx_t_1 = (!feof(__pyx_v_self->infile)); if (!__pyx_t_1) break; - /* "ctabix.pyx":803 + /* "pysam/ctabix.pyx":803 * # getline allocates on demand * # return number of characters read excluding null byte * nbytes = getline( &b, &nbytes, self.infile) # <<<<<<<<<<<<<< @@ -8163,7 +8149,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob */ __pyx_v_nbytes = getline((&__pyx_v_b), (&__pyx_v_nbytes), __pyx_v_self->infile); - /* "ctabix.pyx":805 + /* "pysam/ctabix.pyx":805 * nbytes = getline( &b, &nbytes, self.infile) * # stop at first error * if (nbytes == -1): break # <<<<<<<<<<<<<< @@ -8177,7 +8163,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } __pyx_L5:; - /* "ctabix.pyx":807 + /* "pysam/ctabix.pyx":807 * if (nbytes == -1): break * # skip comments * if (b[0] == '#'): continue # <<<<<<<<<<<<<< @@ -8191,7 +8177,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } __pyx_L6:; - /* "ctabix.pyx":810 + /* "pysam/ctabix.pyx":810 * * # skip empty lines * if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # <<<<<<<<<<<<<< @@ -8217,7 +8203,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } __pyx_L7:; - /* "ctabix.pyx":813 + /* "pysam/ctabix.pyx":813 * * # make sure that entry is complete * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # <<<<<<<<<<<<<< @@ -8233,7 +8219,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } if (__pyx_t_4) { - /* "ctabix.pyx":814 + /* "pysam/ctabix.pyx":814 * # make sure that entry is complete * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': * result = b # <<<<<<<<<<<<<< @@ -8242,7 +8228,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob */ __pyx_v_result = __pyx_v_b; - /* "ctabix.pyx":815 + /* "pysam/ctabix.pyx":815 * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': * result = b * free(b) # <<<<<<<<<<<<<< @@ -8251,7 +8237,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob */ free(__pyx_v_b); - /* "ctabix.pyx":816 + /* "pysam/ctabix.pyx":816 * result = b * free(b) * raise ValueError( "incomplete line at %s" % result ) # <<<<<<<<<<<<<< @@ -8278,7 +8264,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } __pyx_L8:; - /* "ctabix.pyx":823 + /* "pysam/ctabix.pyx":823 * # the wrong memory is freed * # -1 to remove the new-line character * return self.parser(b, nbytes) # <<<<<<<<<<<<<< @@ -8308,7 +8294,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } __pyx_L4_break:; - /* "ctabix.pyx":825 + /* "pysam/ctabix.pyx":825 * return self.parser(b, nbytes) * * free(b) # <<<<<<<<<<<<<< @@ -8317,7 +8303,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob */ free(__pyx_v_b); - /* "ctabix.pyx":826 + /* "pysam/ctabix.pyx":826 * * free(b) * raise StopIteration # <<<<<<<<<<<<<< @@ -8333,7 +8319,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_7); - __Pyx_AddTraceback("ctabix.tabix_copy_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_copy_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -8342,17 +8328,17 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_r = __pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(((struct __pyx_obj_6ctabix_tabix_copy_iterator *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_4__next__(((struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":828 +/* "pysam/ctabix.pyx":828 * raise StopIteration * * def __next__(self): # <<<<<<<<<<<<<< @@ -8360,7 +8346,7 @@ static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__(PyObject *__py * */ -static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -8369,7 +8355,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "ctabix.pyx":829 + /* "pysam/ctabix.pyx":829 * * def __next__(self): * return self.__cnext__() # <<<<<<<<<<<<<< @@ -8377,7 +8363,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o * class tabix_generic_iterator: */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -8387,7 +8373,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("ctabix.tabix_copy_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_copy_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -8396,19 +8382,18 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_6ctabix_22tabix_generic_iterator___init__[] = "tabix_generic_iterator.__init__(self, infile, parser)"; -static PyMethodDef __pyx_mdef_6ctabix_22tabix_generic_iterator_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_22tabix_generic_iterator___init__)}; -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_22tabix_generic_iterator___init__[] = "tabix_generic_iterator.__init__(self, infile, parser)"; +static PyMethodDef __pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_22tabix_generic_iterator___init__)}; +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_infile = 0; PyObject *__pyx_v_parser = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__infile,&__pyx_n_s__parser,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__infile,&__pyx_n_s__parser,0}; PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -8423,18 +8408,15 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *_ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -8457,16 +8439,16 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *_ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_22tabix_generic_iterator___init__(__pyx_self, __pyx_v_self, __pyx_v_infile, __pyx_v_parser); + __pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_generic_iterator___init__(__pyx_self, __pyx_v_self, __pyx_v_infile, __pyx_v_parser); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":836 +/* "pysam/ctabix.pyx":836 * Permits the use of file-like objects for example from the gzip module. * ''' * def __init__(self, infile, parser ): # <<<<<<<<<<<<<< @@ -8474,7 +8456,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *_ * self.infile = infile */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) { +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -8485,7 +8467,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSE int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); - /* "ctabix.pyx":838 + /* "pysam/ctabix.pyx":838 * def __init__(self, infile, parser ): * * self.infile = infile # <<<<<<<<<<<<<< @@ -8494,7 +8476,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSE */ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__infile, __pyx_v_infile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":839 + /* "pysam/ctabix.pyx":839 * * self.infile = infile * if self.infile.closed: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -8518,7 +8500,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSE } __pyx_L3:; - /* "ctabix.pyx":840 + /* "pysam/ctabix.pyx":840 * self.infile = infile * if self.infile.closed: raise ValueError( "I/O operation on closed file." ) * self.parser = parser # <<<<<<<<<<<<<< @@ -8532,7 +8514,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSE __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -8541,20 +8523,19 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSE } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_6ctabix_22tabix_generic_iterator_2__iter__[] = "tabix_generic_iterator.__iter__(self)"; -static PyMethodDef __pyx_mdef_6ctabix_22tabix_generic_iterator_3__iter__ = {__Pyx_NAMESTR("__iter__"), (PyCFunction)__pyx_pw_6ctabix_22tabix_generic_iterator_3__iter__, METH_O, __Pyx_DOCSTR(__pyx_doc_6ctabix_22tabix_generic_iterator_2__iter__)}; -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_22tabix_generic_iterator_2__iter__[] = "tabix_generic_iterator.__iter__(self)"; +static PyMethodDef __pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_3__iter__ = {__Pyx_NAMESTR("__iter__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_3__iter__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_22tabix_generic_iterator_2__iter__)}; +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_3__iter__(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_6ctabix_22tabix_generic_iterator_2__iter__(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":842 +/* "pysam/ctabix.pyx":842 * self.parser = parser * * def __iter__(self): # <<<<<<<<<<<<<< @@ -8562,12 +8543,12 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_3__iter__(PyObject *_ * */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__iter__", 0); - /* "ctabix.pyx":843 + /* "pysam/ctabix.pyx":843 * * def __iter__(self): * return self # <<<<<<<<<<<<<< @@ -8587,20 +8568,19 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUS } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_6ctabix_22tabix_generic_iterator_4__next__[] = "tabix_generic_iterator.__next__(self)"; -static PyMethodDef __pyx_mdef_6ctabix_22tabix_generic_iterator_5__next__ = {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_22tabix_generic_iterator_5__next__, METH_O, __Pyx_DOCSTR(__pyx_doc_6ctabix_22tabix_generic_iterator_4__next__)}; -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_22tabix_generic_iterator_4__next__[] = "tabix_generic_iterator.__next__(self)"; +static PyMethodDef __pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_5__next__ = {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_5__next__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_22tabix_generic_iterator_4__next__)}; +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_5__next__(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":846 +/* "pysam/ctabix.pyx":846 * * # cython version - required for python 3 * def __next__(self): # <<<<<<<<<<<<<< @@ -8608,7 +8588,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_5__next__(PyObject *_ * cdef char * b, * cpy */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { char *__pyx_v_b; char *__pyx_v_cpy; size_t __pyx_v_nbytes; @@ -8631,7 +8611,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "ctabix.pyx":850 + /* "pysam/ctabix.pyx":850 * cdef char * b, * cpy * cdef size_t nbytes * while 1: # <<<<<<<<<<<<<< @@ -8641,7 +8621,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS while (1) { if (!1) break; - /* "ctabix.pyx":852 + /* "pysam/ctabix.pyx":852 * while 1: * * line = self.infile.readline() # <<<<<<<<<<<<<< @@ -8660,7 +8640,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS __pyx_v_line = __pyx_t_1; __pyx_t_1 = 0; - /* "ctabix.pyx":853 + /* "pysam/ctabix.pyx":853 * * line = self.infile.readline() * if not line: break # <<<<<<<<<<<<<< @@ -8675,20 +8655,20 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } __pyx_L5:; - /* "ctabix.pyx":855 + /* "pysam/ctabix.pyx":855 * if not line: break * * s = _force_bytes( line ) # <<<<<<<<<<<<<< * b = s * nbytes = len( line ) */ - __pyx_t_1 = ((PyObject *)__pyx_f_6ctabix__force_bytes(__pyx_v_line)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_6ctabix__force_bytes(__pyx_v_line)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_XDECREF(((PyObject *)__pyx_v_s)); __pyx_v_s = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":856 + /* "pysam/ctabix.pyx":856 * * s = _force_bytes( line ) * b = s # <<<<<<<<<<<<<< @@ -8698,7 +8678,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_s)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_b = __pyx_t_5; - /* "ctabix.pyx":857 + /* "pysam/ctabix.pyx":857 * s = _force_bytes( line ) * b = s * nbytes = len( line ) # <<<<<<<<<<<<<< @@ -8708,7 +8688,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS __pyx_t_6 = PyObject_Length(__pyx_v_line); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_nbytes = __pyx_t_6; - /* "ctabix.pyx":858 + /* "pysam/ctabix.pyx":858 * b = s * nbytes = len( line ) * assert b[nbytes] == '\0' # <<<<<<<<<<<<<< @@ -8722,7 +8702,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } #endif - /* "ctabix.pyx":861 + /* "pysam/ctabix.pyx":861 * * # skip comments * if (b[0] == '#'): continue # <<<<<<<<<<<<<< @@ -8736,7 +8716,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } __pyx_L6:; - /* "ctabix.pyx":864 + /* "pysam/ctabix.pyx":864 * * # skip empty lines * if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # <<<<<<<<<<<<<< @@ -8762,7 +8742,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } __pyx_L7:; - /* "ctabix.pyx":867 + /* "pysam/ctabix.pyx":867 * * # make sure that entry is complete * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # <<<<<<<<<<<<<< @@ -8778,7 +8758,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } if (__pyx_t_8) { - /* "ctabix.pyx":868 + /* "pysam/ctabix.pyx":868 * # make sure that entry is complete * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': * raise ValueError( "incomplete line at %s" % line ) # <<<<<<<<<<<<<< @@ -8802,7 +8782,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } __pyx_L8:; - /* "ctabix.pyx":871 + /* "pysam/ctabix.pyx":871 * * # create a copy * cpy = malloc(nbytes+1) # <<<<<<<<<<<<<< @@ -8811,7 +8791,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS */ __pyx_v_cpy = ((char *)malloc((__pyx_v_nbytes + 1))); - /* "ctabix.pyx":872 + /* "pysam/ctabix.pyx":872 * # create a copy * cpy = malloc(nbytes+1) * if cpy == NULL: raise MemoryError() # <<<<<<<<<<<<<< @@ -8825,7 +8805,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } __pyx_L9:; - /* "ctabix.pyx":873 + /* "pysam/ctabix.pyx":873 * cpy = malloc(nbytes+1) * if cpy == NULL: raise MemoryError() * memcpy( cpy, b, nbytes+1) # <<<<<<<<<<<<<< @@ -8834,7 +8814,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS */ memcpy(__pyx_v_cpy, __pyx_v_b, (__pyx_v_nbytes + 1)); - /* "ctabix.pyx":875 + /* "pysam/ctabix.pyx":875 * memcpy( cpy, b, nbytes+1) * * return self.parser(cpy, nbytes) # <<<<<<<<<<<<<< @@ -8867,7 +8847,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } __pyx_L4_break:; - /* "ctabix.pyx":877 + /* "pysam/ctabix.pyx":877 * return self.parser(cpy, nbytes) * * raise StopIteration # <<<<<<<<<<<<<< @@ -8884,7 +8864,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_9); __Pyx_XDECREF(__pyx_t_10); - __Pyx_AddTraceback("ctabix.tabix_generic_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_generic_iterator.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_line); @@ -8895,20 +8875,19 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_7next(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_6ctabix_22tabix_generic_iterator_6next[] = "tabix_generic_iterator.next(self)"; -static PyMethodDef __pyx_mdef_6ctabix_22tabix_generic_iterator_7next = {__Pyx_NAMESTR("next"), (PyCFunction)__pyx_pw_6ctabix_22tabix_generic_iterator_7next, METH_O, __Pyx_DOCSTR(__pyx_doc_6ctabix_22tabix_generic_iterator_6next)}; -static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_7next(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_7next(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_22tabix_generic_iterator_6next[] = "tabix_generic_iterator.next(self)"; +static PyMethodDef __pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_7next = {__Pyx_NAMESTR("next"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_7next, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_22tabix_generic_iterator_6next)}; +static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_7next(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("next (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_6ctabix_22tabix_generic_iterator_6next(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_6next(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":880 +/* "pysam/ctabix.pyx":880 * * # python version - required for python 2.7 * def next(self): # <<<<<<<<<<<<<< @@ -8916,7 +8895,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_7next(PyObject *__pyx * */ -static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -8926,7 +8905,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED P int __pyx_clineno = 0; __Pyx_RefNannySetupContext("next", 0); - /* "ctabix.pyx":881 + /* "pysam/ctabix.pyx":881 * # python version - required for python 2.7 * def next(self): * return self.__next__() # <<<<<<<<<<<<<< @@ -8948,7 +8927,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED P __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("ctabix.tabix_generic_iterator.next", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_generic_iterator.next", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -8957,18 +8936,17 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED P } /* Python wrapper */ -static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_6ctabix_4tabix_iterator[] = "tabix_iterator(infile, parser)\nreturn an iterator over all entries in a file."; -static PyMethodDef __pyx_mdef_6ctabix_5tabix_iterator = {__Pyx_NAMESTR("tabix_iterator"), (PyCFunction)__pyx_pw_6ctabix_5tabix_iterator, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_4tabix_iterator)}; -static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_6ctabix_4tabix_iterator[] = "tabix_iterator(infile, parser)\nreturn an iterator over all entries in a file."; +static PyMethodDef __pyx_mdef_5pysam_6ctabix_5tabix_iterator = {__Pyx_NAMESTR("tabix_iterator"), (PyCFunction)__pyx_pw_5pysam_6ctabix_5tabix_iterator, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_4tabix_iterator)}; +static PyObject *__pyx_pw_5pysam_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_infile = 0; PyObject *__pyx_v_parser = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("tabix_iterator (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -8982,12 +8960,10 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -9008,16 +8984,16 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("ctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_6ctabix_4tabix_iterator(__pyx_self, __pyx_v_infile, __pyx_v_parser); + __pyx_r = __pyx_pf_5pysam_6ctabix_4tabix_iterator(__pyx_self, __pyx_v_infile, __pyx_v_parser); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "ctabix.pyx":883 +/* "pysam/ctabix.pyx":883 * return self.__next__() * * def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<< @@ -9025,7 +9001,7 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject * return tabix_generic_iterator( infile, parser ) */ -static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) { +static PyObject *__pyx_pf_5pysam_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -9036,7 +9012,7 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("tabix_iterator", 0); - /* "ctabix.pyx":885 + /* "pysam/ctabix.pyx":885 * def tabix_iterator( infile, parser ): * """return an iterator over all entries in a file.""" * return tabix_generic_iterator( infile, parser ) # <<<<<<<<<<<<<< @@ -9068,7 +9044,7 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_ __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("ctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.ctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -9076,21 +9052,21 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_ return __pyx_r; } -static PyObject *__pyx_tp_new_6ctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k) { +static PyObject *__pyx_tp_new_5pysam_6ctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - if (__pyx_pw_6ctabix_9Tabixfile_1__cinit__(o, a, k) < 0) { + if (__pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_6ctabix_Tabixfile(PyObject *o) { +static void __pyx_tp_dealloc_5pysam_6ctabix_Tabixfile(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_6ctabix_9Tabixfile_13__dealloc__(o); + __pyx_pw_5pysam_6ctabix_9Tabixfile_13__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -9098,31 +9074,31 @@ static void __pyx_tp_dealloc_6ctabix_Tabixfile(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } -static PyObject *__pyx_getprop_6ctabix_9Tabixfile_filename(PyObject *o, void *x) { - return __pyx_pw_6ctabix_9Tabixfile_8filename_1__get__(o); +static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_filename(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_6ctabix_9Tabixfile_8filename_1__get__(o); } -static PyObject *__pyx_getprop_6ctabix_9Tabixfile_header(PyObject *o, void *x) { - return __pyx_pw_6ctabix_9Tabixfile_6header_1__get__(o); +static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_header(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_6ctabix_9Tabixfile_6header_1__get__(o); } -static PyObject *__pyx_getprop_6ctabix_9Tabixfile_contigs(PyObject *o, void *x) { - return __pyx_pw_6ctabix_9Tabixfile_7contigs_1__get__(o); +static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_6ctabix_9Tabixfile_7contigs_1__get__(o); } -static PyMethodDef __pyx_methods_6ctabix_Tabixfile[] = { - {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_6ctabix_9Tabixfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile_2_isOpen)}, - {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_6ctabix_9Tabixfile_5_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile_4_open)}, - {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_6ctabix_9Tabixfile_7_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile_6_parseRegion)}, - {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_6ctabix_9Tabixfile_9fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile_8fetch)}, - {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_6ctabix_9Tabixfile_11close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile_10close)}, +static PyMethodDef __pyx_methods_5pysam_6ctabix_Tabixfile[] = { + {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_2_isOpen)}, + {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_4_open)}, + {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_7_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_6_parseRegion)}, + {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_8fetch)}, + {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_11close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_10close)}, {0, 0, 0, 0} }; -static struct PyGetSetDef __pyx_getsets_6ctabix_Tabixfile[] = { - {(char *)"filename", __pyx_getprop_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_59), 0}, - {(char *)"header", __pyx_getprop_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_60), 0}, - {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_61), 0}, +static struct PyGetSetDef __pyx_getsets_5pysam_6ctabix_Tabixfile[] = { + {(char *)"filename", __pyx_getprop_5pysam_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_59), 0}, + {(char *)"header", __pyx_getprop_5pysam_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_60), 0}, + {(char *)"contigs", __pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_61), 0}, {0, 0, 0, 0, 0} }; @@ -9224,12 +9200,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Tabixfile = { #endif }; -static PyTypeObject __pyx_type_6ctabix_Tabixfile = { +static PyTypeObject __pyx_type_5pysam_6ctabix_Tabixfile = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.Tabixfile"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_Tabixfile), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.Tabixfile"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_Tabixfile, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_Tabixfile, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -9256,9 +9232,9 @@ static PyTypeObject __pyx_type_6ctabix_Tabixfile = { 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_6ctabix_Tabixfile, /*tp_methods*/ + __pyx_methods_5pysam_6ctabix_Tabixfile, /*tp_methods*/ 0, /*tp_members*/ - __pyx_getsets_6ctabix_Tabixfile, /*tp_getset*/ + __pyx_getsets_5pysam_6ctabix_Tabixfile, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ @@ -9266,7 +9242,7 @@ static PyTypeObject __pyx_type_6ctabix_Tabixfile = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_Tabixfile, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_Tabixfile, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -9280,21 +9256,21 @@ static PyTypeObject __pyx_type_6ctabix_Tabixfile = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k) { +static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - if (__pyx_pw_6ctabix_13TabixIterator_1__cinit__(o, a, k) < 0) { + if (__pyx_pw_5pysam_6ctabix_13TabixIterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_6ctabix_TabixIterator(PyObject *o) { +static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_6ctabix_13TabixIterator_7__dealloc__(o); + __pyx_pw_5pysam_6ctabix_13TabixIterator_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -9302,8 +9278,8 @@ static void __pyx_tp_dealloc_6ctabix_TabixIterator(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } -static PyMethodDef __pyx_methods_6ctabix_TabixIterator[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_13TabixIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_13TabixIterator_4__next__)}, +static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIterator[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__)}, {0, 0, 0, 0} }; @@ -9405,12 +9381,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TabixIterator = { #endif }; -static PyTypeObject __pyx_type_6ctabix_TabixIterator = { +static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIterator = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.TabixIterator"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_TabixIterator), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.TabixIterator"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_TabixIterator, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -9435,9 +9411,9 @@ static PyTypeObject __pyx_type_6ctabix_TabixIterator = { 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/ - __pyx_pw_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/ - __pyx_methods_6ctabix_TabixIterator, /*tp_methods*/ + __pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/ + __pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/ + __pyx_methods_5pysam_6ctabix_TabixIterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -9447,7 +9423,7 @@ static PyTypeObject __pyx_type_6ctabix_TabixIterator = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_TabixIterator, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_TabixIterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -9461,21 +9437,21 @@ static PyTypeObject __pyx_type_6ctabix_TabixIterator = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) { +static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - if (__pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) { + if (__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_6ctabix_TabixHeaderIterator(PyObject *o) { +static void __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_6ctabix_19TabixHeaderIterator_7__dealloc__(o); + __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -9483,8 +9459,8 @@ static void __pyx_tp_dealloc_6ctabix_TabixHeaderIterator(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } -static PyMethodDef __pyx_methods_6ctabix_TabixHeaderIterator[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixHeaderIterator_4__next__)}, +static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixHeaderIterator[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__)}, {0, 0, 0, 0} }; @@ -9586,12 +9562,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = { #endif }; -static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = { +static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.TabixHeaderIterator"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.TabixHeaderIterator"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_TabixHeaderIterator, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -9616,9 +9592,9 @@ static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = { 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/ - __pyx_pw_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/ - __pyx_methods_6ctabix_TabixHeaderIterator, /*tp_methods*/ + __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/ + __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/ + __pyx_methods_5pysam_6ctabix_TabixHeaderIterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -9628,7 +9604,7 @@ static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_TabixHeaderIterator, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -9642,17 +9618,17 @@ static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) { +static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; return o; } -static void __pyx_tp_dealloc_6ctabix_Parser(PyObject *o) { +static void __pyx_tp_dealloc_5pysam_6ctabix_Parser(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } -static PyMethodDef __pyx_methods_6ctabix_Parser[] = { +static PyMethodDef __pyx_methods_5pysam_6ctabix_Parser[] = { {0, 0, 0, 0} }; @@ -9754,12 +9730,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Parser = { #endif }; -static PyTypeObject __pyx_type_6ctabix_Parser = { +static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.Parser"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_Parser), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.Parser"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -9786,7 +9762,7 @@ static PyTypeObject __pyx_type_6ctabix_Parser = { 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_6ctabix_Parser, /*tp_methods*/ + __pyx_methods_5pysam_6ctabix_Parser, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -9796,7 +9772,7 @@ static PyTypeObject __pyx_type_6ctabix_Parser = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_Parser, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_Parser, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -9810,13 +9786,13 @@ static PyTypeObject __pyx_type_6ctabix_Parser = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) { - PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k); +static PyObject *__pyx_tp_new_5pysam_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } -static PyMethodDef __pyx_methods_6ctabix_asTuple[] = { +static PyMethodDef __pyx_methods_5pysam_6ctabix_asTuple[] = { {0, 0, 0, 0} }; @@ -9918,12 +9894,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asTuple = { #endif }; -static PyTypeObject __pyx_type_6ctabix_asTuple = { +static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.asTuple"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_asTuple), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.asTuple"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -9937,7 +9913,7 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = { &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/ 0, /*tp_hash*/ - __pyx_pw_6ctabix_7asTuple_1__call__, /*tp_call*/ + __pyx_pw_5pysam_6ctabix_7asTuple_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ @@ -9950,7 +9926,7 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = { 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_6ctabix_asTuple, /*tp_methods*/ + __pyx_methods_5pysam_6ctabix_asTuple, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -9960,7 +9936,7 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_asTuple, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_asTuple, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -9974,13 +9950,13 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) { - PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k); +static PyObject *__pyx_tp_new_5pysam_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } -static PyMethodDef __pyx_methods_6ctabix_asGTF[] = { +static PyMethodDef __pyx_methods_5pysam_6ctabix_asGTF[] = { {0, 0, 0, 0} }; @@ -10082,12 +10058,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asGTF = { #endif }; -static PyTypeObject __pyx_type_6ctabix_asGTF = { +static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.asGTF"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_asGTF), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.asGTF"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -10101,7 +10077,7 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = { &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/ 0, /*tp_hash*/ - __pyx_pw_6ctabix_5asGTF_1__call__, /*tp_call*/ + __pyx_pw_5pysam_6ctabix_5asGTF_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ @@ -10114,7 +10090,7 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = { 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_6ctabix_asGTF, /*tp_methods*/ + __pyx_methods_5pysam_6ctabix_asGTF, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -10124,7 +10100,7 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_asGTF, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_asGTF, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -10138,13 +10114,13 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) { - PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k); +static PyObject *__pyx_tp_new_5pysam_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } -static PyMethodDef __pyx_methods_6ctabix_asBed[] = { +static PyMethodDef __pyx_methods_5pysam_6ctabix_asBed[] = { {0, 0, 0, 0} }; @@ -10246,12 +10222,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asBed = { #endif }; -static PyTypeObject __pyx_type_6ctabix_asBed = { +static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.asBed"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_asBed), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.asBed"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -10265,7 +10241,7 @@ static PyTypeObject __pyx_type_6ctabix_asBed = { &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/ 0, /*tp_hash*/ - __pyx_pw_6ctabix_5asBed_1__call__, /*tp_call*/ + __pyx_pw_5pysam_6ctabix_5asBed_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ @@ -10278,7 +10254,7 @@ static PyTypeObject __pyx_type_6ctabix_asBed = { 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_6ctabix_asBed, /*tp_methods*/ + __pyx_methods_5pysam_6ctabix_asBed, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -10288,7 +10264,7 @@ static PyTypeObject __pyx_type_6ctabix_asBed = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_asBed, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_asBed, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -10302,13 +10278,13 @@ static PyTypeObject __pyx_type_6ctabix_asBed = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) { - PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k); +static PyObject *__pyx_tp_new_5pysam_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) { + PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; return o; } -static PyMethodDef __pyx_methods_6ctabix_asVCF[] = { +static PyMethodDef __pyx_methods_5pysam_6ctabix_asVCF[] = { {0, 0, 0, 0} }; @@ -10410,12 +10386,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asVCF = { #endif }; -static PyTypeObject __pyx_type_6ctabix_asVCF = { +static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.asVCF"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_asVCF), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.asVCF"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -10429,7 +10405,7 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = { &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/ 0, /*tp_hash*/ - __pyx_pw_6ctabix_5asVCF_1__call__, /*tp_call*/ + __pyx_pw_5pysam_6ctabix_5asVCF_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ @@ -10442,7 +10418,7 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = { 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_6ctabix_asVCF, /*tp_methods*/ + __pyx_methods_5pysam_6ctabix_asVCF, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -10452,7 +10428,7 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_asVCF, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_asVCF, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -10466,53 +10442,55 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = { #endif }; -static PyObject *__pyx_tp_new_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_6ctabix_TabixIteratorParsed *p; +static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_6ctabix_TabixIteratorParsed *)o); - p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); - if (__pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) { + p = ((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o); + p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); + if (__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) { - struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o; +static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) { + struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o; + PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_6ctabix_19TabixIteratorParsed_7__dealloc__(o); + __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } - Py_XDECREF(((PyObject *)p->parser)); + Py_CLEAR(p->parser); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o; + struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } return 0; } -static int __pyx_tp_clear_6ctabix_TabixIteratorParsed(PyObject *o) { - struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o; +static int __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) { + struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); - p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); + p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } -static PyMethodDef __pyx_methods_6ctabix_TabixIteratorParsed[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixIteratorParsed_4__next__)}, +static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIteratorParsed[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__)}, {0, 0, 0, 0} }; @@ -10614,12 +10592,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = { #endif }; -static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = { +static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.TabixIteratorParsed"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_TabixIteratorParsed), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.TabixIteratorParsed"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_TabixIteratorParsed, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -10640,13 +10618,13 @@ static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = { &__pyx_tp_as_buffer_TabixIteratorParsed, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterates over mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/ - __pyx_tp_traverse_6ctabix_TabixIteratorParsed, /*tp_traverse*/ - __pyx_tp_clear_6ctabix_TabixIteratorParsed, /*tp_clear*/ + __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed, /*tp_traverse*/ + __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/ - __pyx_pw_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/ - __pyx_methods_6ctabix_TabixIteratorParsed, /*tp_methods*/ + __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/ + __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/ + __pyx_methods_5pysam_6ctabix_TabixIteratorParsed, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -10656,7 +10634,7 @@ static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_TabixIteratorParsed, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -10669,56 +10647,58 @@ static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator __pyx_vtable_6ctabix_tabix_inplace_iterator; +static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator __pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator; -static PyObject *__pyx_tp_new_6ctabix_tabix_inplace_iterator(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_6ctabix_tabix_inplace_iterator *p; +static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o); - p->__pyx_vtab = __pyx_vtabptr_6ctabix_tabix_inplace_iterator; - p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); - if (__pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(o, a, k) < 0) { + p = ((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o); + p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator; + p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); + if (__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator(PyObject *o) { - struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o; +static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) { + struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o; + PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_6ctabix_22tabix_inplace_iterator_5__dealloc__(o); + __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } - Py_XDECREF(((PyObject *)p->parser)); + Py_CLEAR(p->parser); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_6ctabix_tabix_inplace_iterator(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o; + struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } return 0; } -static int __pyx_tp_clear_6ctabix_tabix_inplace_iterator(PyObject *o) { - struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o; +static int __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) { + struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); - p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); + p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } -static PyMethodDef __pyx_methods_6ctabix_tabix_inplace_iterator[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)}, +static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; @@ -10820,12 +10800,12 @@ static PyBufferProcs __pyx_tp_as_buffer_tabix_inplace_iterator = { #endif }; -static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = { +static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_inplace_iterator = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.tabix_inplace_iterator"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_tabix_inplace_iterator), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.tabix_inplace_iterator"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -10846,13 +10826,13 @@ static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = { &__pyx_tp_as_buffer_tabix_inplace_iterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not safe. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/ - __pyx_tp_traverse_6ctabix_tabix_inplace_iterator, /*tp_traverse*/ - __pyx_tp_clear_6ctabix_tabix_inplace_iterator, /*tp_clear*/ + __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator, /*tp_traverse*/ + __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_6ctabix_22tabix_inplace_iterator_3__iter__, /*tp_iter*/ - __pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__, /*tp_iternext*/ - __pyx_methods_6ctabix_tabix_inplace_iterator, /*tp_methods*/ + __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_3__iter__, /*tp_iter*/ + __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, /*tp_iternext*/ + __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -10862,7 +10842,7 @@ static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_tabix_inplace_iterator, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -10875,47 +10855,49 @@ static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = { 0, /*tp_version_tag*/ #endif }; -static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator __pyx_vtable_6ctabix_tabix_copy_iterator; +static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator __pyx_vtable_5pysam_6ctabix_tabix_copy_iterator; -static PyObject *__pyx_tp_new_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_6ctabix_tabix_copy_iterator *p; +static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_6ctabix_tabix_copy_iterator *)o); - p->__pyx_vtab = __pyx_vtabptr_6ctabix_tabix_copy_iterator; - p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); - if (__pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(o, a, k) < 0) { + p = ((struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o); + p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator; + p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); + if (__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_6ctabix_tabix_copy_iterator(PyObject *o) { - struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o; - Py_XDECREF(((PyObject *)p->parser)); +static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) { + struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o; + PyObject_GC_UnTrack(o); + Py_CLEAR(p->parser); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_6ctabix_tabix_copy_iterator(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_6ctabix_tabix_copy_iterator(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o; + struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } return 0; } -static int __pyx_tp_clear_6ctabix_tabix_copy_iterator(PyObject *o) { - struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o; +static int __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) { + struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); - p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); + p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } -static PyMethodDef __pyx_methods_6ctabix_tabix_copy_iterator[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)}, +static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_copy_iterator[] = { + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; @@ -11017,12 +10999,12 @@ static PyBufferProcs __pyx_tp_as_buffer_tabix_copy_iterator = { #endif }; -static PyTypeObject __pyx_type_6ctabix_tabix_copy_iterator = { +static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_copy_iterator = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("ctabix.tabix_copy_iterator"), /*tp_name*/ - sizeof(struct __pyx_obj_6ctabix_tabix_copy_iterator), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.ctabix.tabix_copy_iterator"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_6ctabix_tabix_copy_iterator, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -11043,13 +11025,13 @@ static PyTypeObject __pyx_type_6ctabix_tabix_copy_iterator = { &__pyx_tp_as_buffer_tabix_copy_iterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not save. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/ - __pyx_tp_traverse_6ctabix_tabix_copy_iterator, /*tp_traverse*/ - __pyx_tp_clear_6ctabix_tabix_copy_iterator, /*tp_clear*/ + __pyx_tp_traverse_5pysam_6ctabix_tabix_copy_iterator, /*tp_traverse*/ + __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_6ctabix_19tabix_copy_iterator_3__iter__, /*tp_iter*/ - __pyx_pw_6ctabix_19tabix_copy_iterator_5__next__, /*tp_iternext*/ - __pyx_methods_6ctabix_tabix_copy_iterator, /*tp_methods*/ + __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_3__iter__, /*tp_iter*/ + __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__, /*tp_iternext*/ + __pyx_methods_5pysam_6ctabix_tabix_copy_iterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -11059,7 +11041,7 @@ static PyTypeObject __pyx_type_6ctabix_tabix_copy_iterator = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_6ctabix_tabix_copy_iterator, /*tp_new*/ + __pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -11124,9 +11106,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0}, {&__pyx_n_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 1}, {&__pyx_kp_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 0}, + {&__pyx_n_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 1}, {&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0}, - {&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0}, - {&__pyx_n_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 1}, + {&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0}, + {&__pyx_n_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 1}, {&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0}, {&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1}, {&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1}, @@ -11165,7 +11148,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__conf, __pyx_k__conf, sizeof(__pyx_k__conf), 0, 0, 1, 1}, {&__pyx_n_s__conf_data, __pyx_k__conf_data, sizeof(__pyx_k__conf_data), 0, 0, 1, 1}, {&__pyx_n_s__cpy, __pyx_k__cpy, sizeof(__pyx_k__cpy), 0, 0, 1, 1}, - {&__pyx_n_s__ctabix, __pyx_k__ctabix, sizeof(__pyx_k__ctabix), 0, 0, 1, 1}, {&__pyx_n_s__ctypes, __pyx_k__ctypes, sizeof(__pyx_k__ctypes), 0, 0, 1, 1}, {&__pyx_n_s__decode, __pyx_k__decode, sizeof(__pyx_k__decode), 0, 0, 1, 1}, {&__pyx_n_s__encode, __pyx_k__encode, sizeof(__pyx_k__encode), 0, 0, 1, 1}, @@ -11247,7 +11229,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "ctabix.pyx":58 + /* "pysam/ctabix.pyx":58 * return s * elif PyUnicode_Check(s): * return s.encode('ascii') # <<<<<<<<<<<<<< @@ -11261,7 +11243,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2)); - /* "ctabix.pyx":78 + /* "pysam/ctabix.pyx":78 * return s * elif PyBytes_Check(s): * return s.decode('ascii') # <<<<<<<<<<<<<< @@ -11275,7 +11257,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4)); - /* "ctabix.pyx":112 + /* "pysam/ctabix.pyx":112 * * filename_index = filename + ".tbi" * self.isremote = filename.startswith( "http:") or filename.startswith( "ftp:" ) # <<<<<<<<<<<<<< @@ -11295,7 +11277,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10)); - /* "ctabix.pyx":117 + /* "pysam/ctabix.pyx":117 * filename = _my_encodeFilename(filename) * filename_index = _my_encodeFilename(filename_index) * cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<< @@ -11309,7 +11291,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11)); - /* "ctabix.pyx":125 + /* "pysam/ctabix.pyx":125 * if mode[0] == 'w': * # open file for writing * raise NotImplementedError("writing to tabix files not implemented" ) # <<<<<<<<<<<<<< @@ -11323,7 +11305,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_12)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13)); - /* "ctabix.pyx":212 + /* "pysam/ctabix.pyx":212 * * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< @@ -11337,7 +11319,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_22)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23)); - /* "ctabix.pyx":235 + /* "pysam/ctabix.pyx":235 * '''filename associated with this object.''' * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< @@ -11351,7 +11333,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_22)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_24)); - /* "ctabix.pyx":302 + /* "pysam/ctabix.pyx":302 * * if self.iterator == NULL: * raise ValueError("malformatted query or wrong sequence name.\n") # <<<<<<<<<<<<<< @@ -11365,7 +11347,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26)); - /* "ctabix.pyx":347 + /* "pysam/ctabix.pyx":347 * * if self.iterator == NULL: * raise ValueError("can't open header.\n") # <<<<<<<<<<<<<< @@ -11379,7 +11361,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_27)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_28)); - /* "ctabix.pyx":539 + /* "pysam/ctabix.pyx":539 * * if self.iterator == NULL: * raise ValueError("malformatted query or wrong sequence name.\n") # <<<<<<<<<<<<<< @@ -11393,7 +11375,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_29)); - /* "ctabix.pyx":590 + /* "pysam/ctabix.pyx":590 * fp = bgzf_open( fn, "w") * if fp == NULL: * raise IOError( "could not open '%s' for writing" ) # <<<<<<<<<<<<<< @@ -11407,7 +11389,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_33)); - /* "ctabix.pyx":595 + /* "pysam/ctabix.pyx":595 * fd_src = open(fn, O_RDONLY) * if fd_src == 0: * raise IOError( "could not open '%s' for reading" ) # <<<<<<<<<<<<<< @@ -11421,7 +11403,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_34)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35)); - /* "ctabix.pyx":605 + /* "pysam/ctabix.pyx":605 * if r < 0: * free( buffer ) * raise OSError("writing failed") # <<<<<<<<<<<<<< @@ -11435,7 +11417,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_36)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_37)); - /* "ctabix.pyx":609 + /* "pysam/ctabix.pyx":609 * free( buffer ) * r = bgzf_close(fp) * if r < 0: raise OSError("writing failed") # <<<<<<<<<<<<<< @@ -11449,7 +11431,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_36)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_38)); - /* "ctabix.pyx":656 + /* "pysam/ctabix.pyx":656 * * if preset == None and (seq_col == None or start_col == None or end_col == None): * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) # <<<<<<<<<<<<<< @@ -11463,7 +11445,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44)); - /* "ctabix.pyx":658 + /* "pysam/ctabix.pyx":658 * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) * * if not filename.endswith(".gz"): # <<<<<<<<<<<<<< @@ -11477,7 +11459,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_45)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_46)); - /* "ctabix.pyx":664 + /* "pysam/ctabix.pyx":664 * * if not force and os.path.exists(filename + ".tbi" ): * raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" ) # <<<<<<<<<<<<<< @@ -11491,7 +11473,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_47)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48)); - /* "ctabix.pyx":722 + /* "pysam/ctabix.pyx":722 * * cdef int fd = PyObject_AsFileDescriptor( infile ) * if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -11505,7 +11487,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52)); - /* "ctabix.pyx":725 + /* "pysam/ctabix.pyx":725 * self.infile = fdopen( fd, 'r') * * if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -11519,7 +11501,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53)); - /* "ctabix.pyx":783 + /* "pysam/ctabix.pyx":783 * * cdef int fd = PyObject_AsFileDescriptor( infile ) * if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -11533,7 +11515,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55)); - /* "ctabix.pyx":785 + /* "pysam/ctabix.pyx":785 * if fd == -1: raise ValueError( "I/O operation on closed file." ) * self.infile = fdopen( fd, 'r') * if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -11547,7 +11529,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_56)); - /* "ctabix.pyx":839 + /* "pysam/ctabix.pyx":839 * * self.infile = infile * if self.infile.closed: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -11561,7 +11543,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57)); - /* "ctabix.pyx":564 + /* "pysam/ctabix.pyx":564 * ti_iter_destroy(self.iterator) * * def tabix_compress( filename_in, # <<<<<<<<<<<<<< @@ -11606,152 +11588,152 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63)); __pyx_k_codeobj_64 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_compress, 564, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":611 + /* "pysam/ctabix.pyx":611 * if r < 0: raise OSError("writing failed") * * def tabix_index( filename, # <<<<<<<<<<<<<< * force = False, * seq_col = None, */ - __pyx_k_tuple_66 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_66); + __pyx_k_tuple_67 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_67); __Pyx_INCREF(((PyObject *)__pyx_n_s__filename)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 0, ((PyObject *)__pyx_n_s__filename)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 0, ((PyObject *)__pyx_n_s__filename)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename)); __Pyx_INCREF(((PyObject *)__pyx_n_s__force)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 1, ((PyObject *)__pyx_n_s__force)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 1, ((PyObject *)__pyx_n_s__force)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__force)); __Pyx_INCREF(((PyObject *)__pyx_n_s__seq_col)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 2, ((PyObject *)__pyx_n_s__seq_col)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 2, ((PyObject *)__pyx_n_s__seq_col)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__seq_col)); __Pyx_INCREF(((PyObject *)__pyx_n_s__start_col)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 3, ((PyObject *)__pyx_n_s__start_col)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 3, ((PyObject *)__pyx_n_s__start_col)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__start_col)); __Pyx_INCREF(((PyObject *)__pyx_n_s__end_col)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 4, ((PyObject *)__pyx_n_s__end_col)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 4, ((PyObject *)__pyx_n_s__end_col)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__end_col)); __Pyx_INCREF(((PyObject *)__pyx_n_s__preset)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 5, ((PyObject *)__pyx_n_s__preset)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 5, ((PyObject *)__pyx_n_s__preset)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__preset)); __Pyx_INCREF(((PyObject *)__pyx_n_s__meta_char)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 6, ((PyObject *)__pyx_n_s__meta_char)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 6, ((PyObject *)__pyx_n_s__meta_char)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__meta_char)); __Pyx_INCREF(((PyObject *)__pyx_n_s__zerobased)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 7, ((PyObject *)__pyx_n_s__zerobased)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 7, ((PyObject *)__pyx_n_s__zerobased)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__zerobased)); __Pyx_INCREF(((PyObject *)__pyx_n_s__preset2conf)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 8, ((PyObject *)__pyx_n_s__preset2conf)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 8, ((PyObject *)__pyx_n_s__preset2conf)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__preset2conf)); __Pyx_INCREF(((PyObject *)__pyx_n_s__conf_data)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 9, ((PyObject *)__pyx_n_s__conf_data)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 9, ((PyObject *)__pyx_n_s__conf_data)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__conf_data)); __Pyx_INCREF(((PyObject *)__pyx_n_s__conf)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 10, ((PyObject *)__pyx_n_s__conf)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 10, ((PyObject *)__pyx_n_s__conf)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__conf)); __Pyx_INCREF(((PyObject *)__pyx_n_s__fn)); - PyTuple_SET_ITEM(__pyx_k_tuple_66, 11, ((PyObject *)__pyx_n_s__fn)); + PyTuple_SET_ITEM(__pyx_k_tuple_67, 11, ((PyObject *)__pyx_n_s__fn)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fn)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_66)); - __pyx_k_codeobj_67 = (PyObject*)__Pyx_PyCode_New(8, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_index, 611, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67)); + __pyx_k_codeobj_68 = (PyObject*)__Pyx_PyCode_New(8, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_index, 611, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":836 + /* "pysam/ctabix.pyx":836 * Permits the use of file-like objects for example from the gzip module. * ''' * def __init__(self, infile, parser ): # <<<<<<<<<<<<<< * * self.infile = infile */ - __pyx_k_tuple_68 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_68); + __pyx_k_tuple_69 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_69); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_68, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_69, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__infile)); - PyTuple_SET_ITEM(__pyx_k_tuple_68, 1, ((PyObject *)__pyx_n_s__infile)); + PyTuple_SET_ITEM(__pyx_k_tuple_69, 1, ((PyObject *)__pyx_n_s__infile)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__infile)); __Pyx_INCREF(((PyObject *)__pyx_n_s__parser)); - PyTuple_SET_ITEM(__pyx_k_tuple_68, 2, ((PyObject *)__pyx_n_s__parser)); + PyTuple_SET_ITEM(__pyx_k_tuple_69, 2, ((PyObject *)__pyx_n_s__parser)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parser)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68)); - __pyx_k_codeobj_69 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____init__, 836, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_69)); + __pyx_k_codeobj_70 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____init__, 836, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":842 + /* "pysam/ctabix.pyx":842 * self.parser = parser * * def __iter__(self): # <<<<<<<<<<<<<< * return self * */ - __pyx_k_tuple_70 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_70); + __pyx_k_tuple_71 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_71); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_70, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_71, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_70)); - __pyx_k_codeobj_71 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____iter__, 842, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_71)); + __pyx_k_codeobj_72 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____iter__, 842, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":846 + /* "pysam/ctabix.pyx":846 * * # cython version - required for python 3 * def __next__(self): # <<<<<<<<<<<<<< * * cdef char * b, * cpy */ - __pyx_k_tuple_72 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_72); + __pyx_k_tuple_73 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_73); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_72, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_73, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__b)); - PyTuple_SET_ITEM(__pyx_k_tuple_72, 1, ((PyObject *)__pyx_n_s__b)); + PyTuple_SET_ITEM(__pyx_k_tuple_73, 1, ((PyObject *)__pyx_n_s__b)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__b)); __Pyx_INCREF(((PyObject *)__pyx_n_s__cpy)); - PyTuple_SET_ITEM(__pyx_k_tuple_72, 2, ((PyObject *)__pyx_n_s__cpy)); + PyTuple_SET_ITEM(__pyx_k_tuple_73, 2, ((PyObject *)__pyx_n_s__cpy)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cpy)); __Pyx_INCREF(((PyObject *)__pyx_n_s__nbytes)); - PyTuple_SET_ITEM(__pyx_k_tuple_72, 3, ((PyObject *)__pyx_n_s__nbytes)); + PyTuple_SET_ITEM(__pyx_k_tuple_73, 3, ((PyObject *)__pyx_n_s__nbytes)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__nbytes)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_72, 4, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_73, 4, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__s)); - PyTuple_SET_ITEM(__pyx_k_tuple_72, 5, ((PyObject *)__pyx_n_s__s)); + PyTuple_SET_ITEM(__pyx_k_tuple_73, 5, ((PyObject *)__pyx_n_s__s)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72)); - __pyx_k_codeobj_73 = (PyObject*)__Pyx_PyCode_New(1, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____next__, 846, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_73)); + __pyx_k_codeobj_74 = (PyObject*)__Pyx_PyCode_New(1, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_73, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____next__, 846, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":880 + /* "pysam/ctabix.pyx":880 * * # python version - required for python 2.7 * def next(self): # <<<<<<<<<<<<<< * return self.__next__() * */ - __pyx_k_tuple_74 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_74); + __pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_75); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_74, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_74)); - __pyx_k_codeobj_75 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__next, 880, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75)); + __pyx_k_codeobj_76 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__next, 880, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "ctabix.pyx":883 + /* "pysam/ctabix.pyx":883 * return self.__next__() * * def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<< * """return an iterator over all entries in a file.""" * return tabix_generic_iterator( infile, parser ) */ - __pyx_k_tuple_77 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_77); + __pyx_k_tuple_78 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_78); __Pyx_INCREF(((PyObject *)__pyx_n_s__infile)); - PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_n_s__infile)); + PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_n_s__infile)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__infile)); __Pyx_INCREF(((PyObject *)__pyx_n_s__parser)); - PyTuple_SET_ITEM(__pyx_k_tuple_77, 1, ((PyObject *)__pyx_n_s__parser)); + PyTuple_SET_ITEM(__pyx_k_tuple_78, 1, ((PyObject *)__pyx_n_s__parser)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parser)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77)); - __pyx_k_codeobj_78 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_iterator, 883, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78)); + __pyx_k_codeobj_79 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_iterator, 883, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -11821,20 +11803,27 @@ PyMODINIT_FUNC PyInit_ctabix(void) #endif /*--- Module creation code ---*/ #if PY_MAJOR_VERSION < 3 - __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION); + __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); #else __pyx_m = PyModule_Create(&__pyx_moduledef); #endif - if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; - #if PY_MAJOR_VERSION < 3 - Py_INCREF(__pyx_m); + if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if PY_MAJOR_VERSION >= 3 + { + PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!PyDict_GetItemString(modules, "pysam.ctabix")) { + if (unlikely(PyDict_SetItemString(modules, "pysam.ctabix", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + } + #endif + __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_PYPY + Py_INCREF(__pyx_b); #endif - __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); - if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; /*--- Initialize various global constants etc. ---*/ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__pyx_module_is_main_ctabix) { + if (__pyx_module_is_main_pysam__ctabix) { if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; } /*--- Builtin init code ---*/ @@ -11842,100 +11831,113 @@ PyMODINIT_FUNC PyInit_ctabix(void) /*--- Constants init code ---*/ if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Global init code ---*/ - __pyx_v_6ctabix__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None); + __pyx_v_5pysam_6ctabix__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None); /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - if (PyType_Ready(&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_Tabixfile = &__pyx_type_6ctabix_Tabixfile; - if (PyType_Ready(&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_5pysam_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_Tabixfile = &__pyx_type_5pysam_6ctabix_Tabixfile; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_CPYTHON { - PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_6ctabix_13TabixIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_6ctabix_13TabixIterator_4__next__.doc = __pyx_doc_6ctabix_13TabixIterator_4__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_13TabixIterator_4__next__; + __pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__.doc = __pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__; } } - if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_TabixIterator = &__pyx_type_6ctabix_TabixIterator; - if (PyType_Ready(&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_TabixIterator = &__pyx_type_5pysam_6ctabix_TabixIterator; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_CPYTHON { - PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_6ctabix_19TabixHeaderIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_6ctabix_19TabixHeaderIterator_4__next__.doc = __pyx_doc_6ctabix_19TabixHeaderIterator_4__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixHeaderIterator_4__next__; + __pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__.doc = __pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__; } } - if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_TabixHeaderIterator = &__pyx_type_6ctabix_TabixHeaderIterator; - if (PyType_Ready(&__pyx_type_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "Parser", (PyObject *)&__pyx_type_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_Parser = &__pyx_type_6ctabix_Parser; - __pyx_type_6ctabix_asTuple.tp_base = __pyx_ptype_6ctabix_Parser; - if (PyType_Ready(&__pyx_type_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "asTuple", (PyObject *)&__pyx_type_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asTuple = &__pyx_type_6ctabix_asTuple; - __pyx_type_6ctabix_asGTF.tp_base = __pyx_ptype_6ctabix_Parser; - if (PyType_Ready(&__pyx_type_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "asGTF", (PyObject *)&__pyx_type_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asGTF = &__pyx_type_6ctabix_asGTF; - __pyx_type_6ctabix_asBed.tp_base = __pyx_ptype_6ctabix_Parser; - if (PyType_Ready(&__pyx_type_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "asBed", (PyObject *)&__pyx_type_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asBed = &__pyx_type_6ctabix_asBed; - __pyx_type_6ctabix_asVCF.tp_base = __pyx_ptype_6ctabix_Parser; - if (PyType_Ready(&__pyx_type_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asVCF = &__pyx_type_6ctabix_asVCF; - if (PyType_Ready(&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = &__pyx_type_5pysam_6ctabix_TabixHeaderIterator; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "Parser", (PyObject *)&__pyx_type_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_Parser = &__pyx_type_5pysam_6ctabix_Parser; + __pyx_type_5pysam_6ctabix_asTuple.tp_base = __pyx_ptype_5pysam_6ctabix_Parser; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "asTuple", (PyObject *)&__pyx_type_5pysam_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asTuple = &__pyx_type_5pysam_6ctabix_asTuple; + __pyx_type_5pysam_6ctabix_asGTF.tp_base = __pyx_ptype_5pysam_6ctabix_Parser; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "asGTF", (PyObject *)&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asGTF = &__pyx_type_5pysam_6ctabix_asGTF; + __pyx_type_5pysam_6ctabix_asBed.tp_base = __pyx_ptype_5pysam_6ctabix_Parser; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "asBed", (PyObject *)&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asBed = &__pyx_type_5pysam_6ctabix_asBed; + __pyx_type_5pysam_6ctabix_asVCF.tp_base = __pyx_ptype_5pysam_6ctabix_Parser; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asVCF = &__pyx_type_5pysam_6ctabix_asVCF; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_CPYTHON { - PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__.doc = __pyx_doc_6ctabix_19TabixIteratorParsed_4__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__; + __pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__.doc = __pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__; } } - if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_TabixIteratorParsed = &__pyx_type_6ctabix_TabixIteratorParsed; - __pyx_vtabptr_6ctabix_tabix_inplace_iterator = &__pyx_vtable_6ctabix_tabix_inplace_iterator; - __pyx_vtable_6ctabix_tabix_inplace_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *))__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__; - if (PyType_Ready(&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_tabix_inplace_iterator = &__pyx_type_6ctabix_tabix_inplace_iterator; - __pyx_vtabptr_6ctabix_tabix_copy_iterator = &__pyx_vtable_6ctabix_tabix_copy_iterator; - __pyx_vtable_6ctabix_tabix_copy_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_copy_iterator *))__pyx_f_6ctabix_19tabix_copy_iterator___cnext__; - if (PyType_Ready(&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_tabix_copy_iterator = &__pyx_type_6ctabix_tabix_copy_iterator; + #endif + if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = &__pyx_type_5pysam_6ctabix_TabixIteratorParsed; + __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator; + __pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *))__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_type_5pysam_6ctabix_tabix_inplace_iterator; + __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_copy_iterator; + __pyx_vtable_5pysam_6ctabix_tabix_copy_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *))__pyx_f_5pysam_6ctabix_19tabix_copy_iterator___cnext__; + if (PyType_Ready(&__pyx_type_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = &__pyx_type_5pysam_6ctabix_tabix_copy_iterator; /*--- Type import code ---*/ - __pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_TupleProxy = __Pyx_ImportType("pysam.TabProxies", "TupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_GTFProxy = __Pyx_ImportType("pysam.TabProxies", "GTFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = __Pyx_ImportType("pysam.TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_BedProxy = __Pyx_ImportType("pysam.TabProxies", "BedProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_BedProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_VCFProxy = __Pyx_ImportType("pysam.TabProxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", + #if CYTHON_COMPILING_IN_PYPY + sizeof(PyTypeObject), + #else + sizeof(PyHeapTypeObject), + #endif + 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ - /* "ctabix.pyx":6 + /* "pysam/ctabix.pyx":6 * # Helper functions for python 3 compatibility - taken * # from csamtools.pyx * import tempfile, os, sys, types, itertools, struct, ctypes, gzip # <<<<<<<<<<<<<< * import io - * cimport TabProxies + * from pysam cimport TabProxies */ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__tempfile), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -11970,11 +11972,11 @@ PyMODINIT_FUNC PyInit_ctabix(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s__gzip, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":7 + /* "pysam/ctabix.pyx":7 * # from csamtools.pyx * import tempfile, os, sys, types, itertools, struct, ctypes, gzip * import io # <<<<<<<<<<<<<< - * cimport TabProxies + * from pysam cimport TabProxies * */ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__io), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -11982,7 +11984,7 @@ PyMODINIT_FUNC PyInit_ctabix(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s__io, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":14 + /* "pysam/ctabix.pyx":14 * PyObject_AsFileDescriptor * * PYTHON3 = PY_MAJOR_VERSION >= 3 # <<<<<<<<<<<<<< @@ -11994,7 +11996,7 @@ PyMODINIT_FUNC PyInit_ctabix(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s__PYTHON3, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":27 + /* "pysam/ctabix.pyx":27 * # filename encoding (copied from lxml.etree.pyx) * cdef str _FILENAME_ENCODING * _FILENAME_ENCODING = sys.getfilesystemencoding() # <<<<<<<<<<<<<< @@ -12010,23 +12012,23 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_XGOTREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); - __Pyx_DECREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); + __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); + __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); __Pyx_GIVEREF(__pyx_t_1); - __pyx_v_6ctabix__FILENAME_ENCODING = ((PyObject*)__pyx_t_1); + __pyx_v_5pysam_6ctabix__FILENAME_ENCODING = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":28 + /* "pysam/ctabix.pyx":28 * cdef str _FILENAME_ENCODING * _FILENAME_ENCODING = sys.getfilesystemencoding() * if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<< * _FILENAME_ENCODING = sys.getdefaultencoding() * if _FILENAME_ENCODING is None: */ - __pyx_t_3 = (__pyx_v_6ctabix__FILENAME_ENCODING == ((PyObject*)Py_None)); + __pyx_t_3 = (__pyx_v_5pysam_6ctabix__FILENAME_ENCODING == ((PyObject*)Py_None)); if (__pyx_t_3) { - /* "ctabix.pyx":29 + /* "pysam/ctabix.pyx":29 * _FILENAME_ENCODING = sys.getfilesystemencoding() * if _FILENAME_ENCODING is None: * _FILENAME_ENCODING = sys.getdefaultencoding() # <<<<<<<<<<<<<< @@ -12042,26 +12044,26 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_XGOTREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); - __Pyx_DECREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); + __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); + __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); __Pyx_GIVEREF(__pyx_t_1); - __pyx_v_6ctabix__FILENAME_ENCODING = ((PyObject*)__pyx_t_1); + __pyx_v_5pysam_6ctabix__FILENAME_ENCODING = ((PyObject*)__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L2; } __pyx_L2:; - /* "ctabix.pyx":30 + /* "pysam/ctabix.pyx":30 * if _FILENAME_ENCODING is None: * _FILENAME_ENCODING = sys.getdefaultencoding() * if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<< * _FILENAME_ENCODING = 'ascii' * */ - __pyx_t_3 = (__pyx_v_6ctabix__FILENAME_ENCODING == ((PyObject*)Py_None)); + __pyx_t_3 = (__pyx_v_5pysam_6ctabix__FILENAME_ENCODING == ((PyObject*)Py_None)); if (__pyx_t_3) { - /* "ctabix.pyx":31 + /* "pysam/ctabix.pyx":31 * _FILENAME_ENCODING = sys.getdefaultencoding() * if _FILENAME_ENCODING is None: * _FILENAME_ENCODING = 'ascii' # <<<<<<<<<<<<<< @@ -12069,15 +12071,15 @@ PyMODINIT_FUNC PyInit_ctabix(void) * #cdef char* _C_FILENAME_ENCODING */ __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii)); - __Pyx_XGOTREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); - __Pyx_DECREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING)); + __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); + __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); - __pyx_v_6ctabix__FILENAME_ENCODING = __pyx_n_s__ascii; + __pyx_v_5pysam_6ctabix__FILENAME_ENCODING = __pyx_n_s__ascii; goto __pyx_L3; } __pyx_L3:; - /* "ctabix.pyx":566 + /* "pysam/ctabix.pyx":566 * def tabix_compress( filename_in, * filename_out, * force = False ): # <<<<<<<<<<<<<< @@ -12090,19 +12092,19 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":564 + /* "pysam/ctabix.pyx":564 * ti_iter_destroy(self.iterator) * * def tabix_compress( filename_in, # <<<<<<<<<<<<<< * filename_out, * force = False ): */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_6ctabix_1tabix_compress, NULL, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_1tabix_compress, NULL, __pyx_n_s_66); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_compress, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":612 + /* "pysam/ctabix.pyx":612 * * def tabix_index( filename, * force = False, # <<<<<<<<<<<<<< @@ -12115,7 +12117,7 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":618 + /* "pysam/ctabix.pyx":618 * preset = None, * meta_char = "#", * zerobased = False, # <<<<<<<<<<<<<< @@ -12128,19 +12130,19 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":611 + /* "pysam/ctabix.pyx":611 * if r < 0: raise OSError("writing failed") * * def tabix_index( filename, # <<<<<<<<<<<<<< * force = False, * seq_col = None, */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_6ctabix_3tabix_index, NULL, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_3tabix_index, NULL, __pyx_n_s_66); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_index, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":831 + /* "pysam/ctabix.pyx":831 * return self.__cnext__() * * class tabix_generic_iterator: # <<<<<<<<<<<<<< @@ -12150,81 +12152,81 @@ PyMODINIT_FUNC PyInit_ctabix(void) __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - /* "ctabix.pyx":836 + /* "pysam/ctabix.pyx":836 * Permits the use of file-like objects for example from the gzip module. * ''' * def __init__(self, infile, parser ): # <<<<<<<<<<<<<< * * self.infile = infile */ - __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_1__init__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_69)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_1__init__, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_70)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "ctabix.pyx":842 + /* "pysam/ctabix.pyx":842 * self.parser = parser * * def __iter__(self): # <<<<<<<<<<<<<< * return self * */ - __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_3__iter__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_71)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_3__iter__, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_72)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____iter__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "ctabix.pyx":846 + /* "pysam/ctabix.pyx":846 * * # cython version - required for python 3 * def __next__(self): # <<<<<<<<<<<<<< * * cdef char * b, * cpy */ - __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_5__next__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_73)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_5__next__, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_74)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____next__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "ctabix.pyx":880 + /* "pysam/ctabix.pyx":880 * * # python version - required for python 2.7 * def next(self): # <<<<<<<<<<<<<< * return self.__next__() * */ - __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_7next, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_75)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_7next, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_76)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__next, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "ctabix.pyx":831 + /* "pysam/ctabix.pyx":831 * return self.__cnext__() * * class tabix_generic_iterator: # <<<<<<<<<<<<<< * '''iterate over ``infile``. * */ - if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_76)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s_58, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_77)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s_58, __pyx_n_s_66); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyObject_SetAttr(__pyx_m, __pyx_n_s_58, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "ctabix.pyx":883 + /* "pysam/ctabix.pyx":883 * return self.__next__() * * def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<< * """return an iterator over all entries in a file.""" * return tabix_generic_iterator( infile, parser ) */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_6ctabix_5tabix_iterator, NULL, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_5tabix_iterator, NULL, __pyx_n_s_66); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_iterator, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":899 + /* "pysam/ctabix.pyx":899 * # return tabix_generic_iterator( infile, parser ) * * __all__ = ["tabix_index", # <<<<<<<<<<<<<< @@ -12257,13 +12259,13 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_iterator)); PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__tabix_iterator)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__tabix_iterator)); - __Pyx_INCREF(((PyObject *)__pyx_n_s_79)); - PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_79)); - __Pyx_GIVEREF(((PyObject *)__pyx_n_s_79)); + __Pyx_INCREF(((PyObject *)__pyx_n_s_80)); + PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_80)); + __Pyx_GIVEREF(((PyObject *)__pyx_n_s_80)); if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "ctabix.pyx":1 + /* "pysam/ctabix.pyx":1 * # cython: embedsignature=True # <<<<<<<<<<<<<< * # adds doc-strings for sphinx * @@ -12277,10 +12279,10 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); if (__pyx_m) { - __Pyx_AddTraceback("init ctabix", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("init pysam.ctabix", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_ImportError, "init ctabix"); + PyErr_SetString(PyExc_ImportError, "init pysam.ctabix"); } __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -12323,6 +12325,32 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) { return result; } +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + Py_ssize_t length; + if (unlikely((start < 0) | (stop < 0))) { + length = strlen(cstring); + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + length = stop - start; + if (unlikely(length <= 0)) + return PyUnicode_FromUnicode(NULL, 0); + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; @@ -12358,33 +12386,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); - Py_XINCREF(value); - Py_XINCREF(tb); - if (tb == Py_None) { - Py_DECREF(tb); - tb = 0; - } - else if (tb != NULL && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - if (value == NULL) { - value = Py_None; + if (!value || value == Py_None) + value = NULL; + else Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } } #if PY_VERSION_HEX < 0x02050000 - if (!PyClass_Check(type)) + if (PyClass_Check(type)) { #else - if (!PyType_Check(type)) + if (PyType_Check(type)) { #endif - { - if (value != Py_None) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } - Py_DECREF(value); value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { @@ -12417,6 +12450,7 @@ raise_error: } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { @@ -12434,12 +12468,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } value = type; type = (PyObject*) Py_TYPE(value); - } else if (!PyExceptionClass_Check(type)) { + } else if (PyExceptionClass_Check(type)) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } + else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyEval_CallObject(type, args); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } - if (cause) { + if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); @@ -12456,9 +12514,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject "BaseException"); goto bad; } - if (!value) { - value = PyObject_CallObject(type, NULL); - } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); @@ -12472,6 +12527,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } } bad: + Py_XDECREF(owned_instance); return; } #endif @@ -12485,7 +12541,7 @@ static void __Pyx_RaiseDoubleKeywordsError( "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AS_STRING(kw_name)); + PyString_AsString(kw_name)); #endif } @@ -12506,48 +12562,72 @@ static int __Pyx_ParseOptionalKeywords( while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; - } else { - #if PY_MAJOR_VERSION < 3 - if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { - #else - if (unlikely(!PyUnicode_Check(key))) { - #endif - goto invalid_keyword_type; - } else { - for (name = first_kw_arg; *name; name++) { - #if PY_MAJOR_VERSION >= 3 - if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && - PyUnicode_Compare(**name, key) == 0) break; - #else - if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && - _PyString_Eq(**name, key)) break; - #endif - } - if (*name) { + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { values[name-argnames] = value; - } else { - for (name=argnames; name != first_kw_arg; name++) { - if (**name == key) goto arg_passed_twice; - #if PY_MAJOR_VERSION >= 3 - if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && - PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice; - #else - if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && - _PyString_Eq(**name, key)) goto arg_passed_twice; - #endif - } - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; } } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; } } return 0; arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, **name); + __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, @@ -12586,22 +12666,54 @@ static void __Pyx_RaiseArgtupleInvalid( more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, - "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)", + "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } - +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, - "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack", + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected); +static CYTHON_INLINE int __Pyx_IterFinish(void) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + PyObject* exc_type = tstate->curexc_type; + if (unlikely(exc_type)) { + if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { + PyObject *exc_value, *exc_tb; + exc_value = tstate->curexc_value; + exc_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; + Py_DECREF(exc_type); + Py_XDECREF(exc_value); + Py_XDECREF(exc_tb); + return 0; + } else { + return -1; + } + } + return 0; +#else + if (unlikely(PyErr_Occurred())) { + if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { + PyErr_Clear(); + return 0; + } else { + return -1; + } + } + return 0; +#endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { @@ -12609,13 +12721,8 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; - } else if (PyErr_Occurred()) { - if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { - PyErr_Clear(); - return 0; - } else { - return -1; - } + } else { + return __Pyx_IterFinish(); } return 0; } @@ -12640,12 +12747,9 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed return 0; } -static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable"); -} - static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; @@ -12654,19 +12758,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif - *type = local_type; - *value = local_value; - *tb = local_tb; Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; @@ -12674,10 +12786,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF - these objects (XDECREF may run arbitrary code). */ + these objects (DECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif return 0; bad: *type = 0; @@ -12690,6 +12805,7 @@ bad: } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; @@ -12697,8 +12813,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; @@ -12710,6 +12830,9 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(type, value, tb); +#endif } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { @@ -12783,7 +12906,6 @@ bad: static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { PyObject *metaclass; - /* Default metaclass */ #if PY_MAJOR_VERSION < 3 if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); @@ -12813,7 +12935,6 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na PyObject *metaclass; if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; - /* Python2 __metaclass__ */ metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { Py_INCREF(metaclass); @@ -13105,6 +13226,56 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) PyString_AsString(func_name), (void *)op); #endif } +#if CYTHON_COMPILING_IN_PYPY +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyCFunctionObject* f = (PyCFunctionObject*)func; + PyCFunction meth = PyCFunction_GET_FUNCTION(func); + PyObject *self = PyCFunction_GET_SELF(func); + Py_ssize_t size; + switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) { + case METH_VARARGS: + if (likely(kw == NULL) || PyDict_Size(kw) == 0) + return (*meth)(self, arg); + break; + case METH_VARARGS | METH_KEYWORDS: + return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); + case METH_NOARGS: + if (likely(kw == NULL) || PyDict_Size(kw) == 0) { + size = PyTuple_GET_SIZE(arg); + if (size == 0) + return (*meth)(self, NULL); + PyErr_Format(PyExc_TypeError, + "%.200s() takes no arguments (%zd given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + case METH_O: + if (likely(kw == NULL) || PyDict_Size(kw) == 0) { + size = PyTuple_GET_SIZE(arg); + if (size == 1) + return (*meth)(self, PyTuple_GET_ITEM(arg, 0)); + PyErr_Format(PyExc_TypeError, + "%.200s() takes exactly one argument (%zd given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + default: + PyErr_SetString(PyExc_SystemError, "Bad call flags in " + "__Pyx_CyFunction_Call. METH_OLDARGS is no " + "longer supported!"); + return NULL; + } + PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", + f->m_ml->ml_name); + return NULL; +} +#else +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + return PyCFunction_Call(func, arg, kw); +} +#endif static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ @@ -13124,7 +13295,7 @@ static PyTypeObject __pyx_CyFunctionType_type = { 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ - __Pyx_PyCFunction_Call, /*tp_call*/ + __Pyx_CyFunction_Call, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ @@ -13160,15 +13331,16 @@ static PyTypeObject __pyx_CyFunctionType_type = { 0, /*tp_version_tag*/ #endif }; -static int __Pyx_CyFunction_init(void) -{ +static int __Pyx_CyFunction_init(void) { +#if !CYTHON_COMPILING_IN_PYPY + __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; +#endif if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; } -void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) -{ +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults = PyMem_Malloc(size); if (!m->defaults) @@ -13177,85 +13349,12 @@ void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) m->defaults_pyobjects = pyobjects; return m->defaults; } -static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) -{ +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults_tuple = tuple; Py_INCREF(tuple); } -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) { - return (equals == Py_NE); - } else if (PyBytes_GET_SIZE(s1) == 1) { - if (equals == Py_EQ) - return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]); - else - return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]); - } else { - int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1)); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -} - -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { - #if CYTHON_PEP393_ENABLED - if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0)) - return -1; - if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) { - return (equals == Py_NE); - } else if (PyUnicode_GET_LENGTH(s1) == 1) { - Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0); - Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0); - return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); - #else - if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { - return (equals == Py_NE); - } else if (PyUnicode_GET_SIZE(s1) == 1) { - Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0]; - Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0]; - return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); - #endif - } else { - int result = PyUnicode_Compare(s1, s2); - if ((result == -1) && unlikely(PyErr_Occurred())) - return -1; - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -} - static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0; const int is_unsigned = const_zero < neg_one; @@ -13285,6 +13384,10 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { else return (int32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { + #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); + #else int32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 @@ -13304,6 +13407,7 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { if (likely(!ret)) return val; } + #endif return (int32_t)-1; } } @@ -13744,6 +13848,23 @@ bad: return -1; } +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, @@ -13796,23 +13917,6 @@ bad: } #endif -#ifndef __PYX_HAVE_RT_ImportModule -#define __PYX_HAVE_RT_ImportModule -static PyObject *__Pyx_ImportModule(const char *name) { - PyObject *py_name = 0; - PyObject *py_module = 0; - py_name = __Pyx_PyIdentifier_FromString(name); - if (!py_name) - goto bad; - py_module = PyImport_Import(py_name); - Py_DECREF(py_name); - return py_module; -bad: - Py_XDECREF(py_name); - return 0; -} -#endif - static void* __Pyx_GetVtable(PyObject *dict) { void* ptr; PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__"); diff --git a/pysam/ctabix.pyx b/pysam/ctabix.pyx index 6a19541..67e8514 100644 --- a/pysam/ctabix.pyx +++ b/pysam/ctabix.pyx @@ -5,7 +5,7 @@ # from csamtools.pyx import tempfile, os, sys, types, itertools, struct, ctypes, gzip import io -cimport TabProxies +from pysam cimport TabProxies from cpython cimport PyErr_SetString, PyBytes_Check, \ PyUnicode_Check, PyBytes_FromStringAndSize, \ diff --git a/pysam/cvcf.c b/pysam/cvcf.c index 6caaba0..1754ba8 100644 --- a/pysam/cvcf.c +++ b/pysam/cvcf.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.16 on Mon Nov 19 08:44:41 2012 */ +/* Generated by Cython 0.17.4 on Wed Jan 23 22:59:29 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -11,7 +11,6 @@ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif - #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall @@ -23,22 +22,18 @@ #define __fastcall #endif #endif - #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif - #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif - #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif - #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 @@ -46,28 +41,28 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif - -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyCFunction_Call PyObject_Call -#else - #define __Pyx_PyCFunction_Call PyCFunction_Call -#endif - #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" + #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) - #define PyNumber_Index(o) PyNumber_Int(o) - #define PyIndex_Check(o) PyNumber_Check(o) + #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ + (PyErr_Format(PyExc_TypeError, \ + "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ + (PyObject*)0)) + #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ + !PyComplex_Check(o)) + #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" + #define CYTHON_FORMAT_SSIZE_T "z" + #define __Pyx_PyIndex_Check PyIndex_Check #endif - #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) @@ -75,7 +70,6 @@ #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) - typedef struct { void *buf; PyObject *obj; @@ -89,7 +83,6 @@ Py_ssize_t *suboffsets; void *internal; } Py_buffer; - #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 @@ -101,11 +94,9 @@ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) - typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif - #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ @@ -115,31 +106,30 @@ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif - #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif - #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif - #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif - - -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH) +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #endif - #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject @@ -147,7 +137,6 @@ #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif - #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type @@ -166,7 +155,6 @@ #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif - #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) @@ -174,9 +162,7 @@ #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif - #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) - #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type @@ -193,11 +179,9 @@ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif - #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif - #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong @@ -206,7 +190,6 @@ #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif - #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) @@ -225,11 +208,9 @@ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif - #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif - #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) @@ -239,7 +220,6 @@ #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif - #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) @@ -248,6 +228,7 @@ #define __Pyx_DOCSTR(n) (n) #endif + #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) @@ -268,8 +249,8 @@ #define _USE_MATH_DEFINES #endif #include -#define __PYX_HAVE__cvcf -#define __PYX_HAVE_API__cvcf +#define __PYX_HAVE__pysam__cvcf +#define __PYX_HAVE_API__pysam__cvcf #include "stdlib.h" #include "string.h" #include "stdint.h" @@ -335,7 +316,11 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); +#if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ @@ -369,27 +354,27 @@ static const char *__pyx_f[] = { }; /*--- Type declarations ---*/ -struct __pyx_obj_6ctabix_Parser; -struct __pyx_obj_6ctabix_asVCF; -struct __pyx_obj_10TabProxies_TupleProxy; -struct __pyx_obj_10TabProxies_NamedTupleProxy; -struct __pyx_obj_10TabProxies_BedProxy; -struct __pyx_obj_6ctabix_tabix_copy_iterator; -struct __pyx_obj_4cvcf_VCFRecord; -struct __pyx_obj_10TabProxies_VCFProxy; -struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse; -struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data; -struct __pyx_obj_6ctabix_TabixIterator; -struct __pyx_obj_4cvcf_asVCFRecord; -struct __pyx_obj_10TabProxies_GTFProxy; -struct __pyx_obj_6ctabix_TabixIteratorParsed; -struct __pyx_obj_6ctabix_TabixHeaderIterator; -struct __pyx_obj_6ctabix_Tabixfile; -struct __pyx_obj_6ctabix_asGTF; -struct __pyx_obj_6ctabix_asBed; -struct __pyx_obj_6ctabix_tabix_inplace_iterator; -struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr; -struct __pyx_obj_6ctabix_asTuple; +struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data; +struct __pyx_obj_5pysam_10TabProxies_TupleProxy; +struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy; +struct __pyx_obj_5pysam_10TabProxies_BedProxy; +struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator; +struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed; +struct __pyx_obj_5pysam_6ctabix_TabixIterator; +struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator; +struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr; +struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse; +struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator; +struct __pyx_obj_5pysam_6ctabix_Parser; +struct __pyx_obj_5pysam_4cvcf_asVCFRecord; +struct __pyx_obj_5pysam_6ctabix_Tabixfile; +struct __pyx_obj_5pysam_6ctabix_asBed; +struct __pyx_obj_5pysam_6ctabix_asGTF; +struct __pyx_obj_5pysam_10TabProxies_VCFProxy; +struct __pyx_obj_5pysam_4cvcf_VCFRecord; +struct __pyx_obj_5pysam_6ctabix_asTuple; +struct __pyx_obj_5pysam_10TabProxies_GTFProxy; +struct __pyx_obj_5pysam_6ctabix_asVCF; struct __pyx_defaults; typedef struct __pyx_defaults __pyx_defaults; struct __pyx_defaults1; @@ -417,27 +402,16 @@ struct __pyx_defaults4 { PyObject *__pyx_arg_lineparse; }; -/* "ctabix.pxd":190 - * cdef tabix_t * tabixfile - * - * cdef class Parser: # <<<<<<<<<<<<<< - * pass +/* "pysam/cvcf.pyx":647 + * return False * + * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< + * cols = line.split('\t') + * if len(cols) != len(self._samples)+9: */ -struct __pyx_obj_6ctabix_Parser { +struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data { PyObject_HEAD -}; - - -/* "ctabix.pxd":202 - * pass - * - * cdef class asVCF(Parser): # <<<<<<<<<<<<<< - * pass - * - */ -struct __pyx_obj_6ctabix_asVCF { - struct __pyx_obj_6ctabix_Parser __pyx_base; + PyObject *__pyx_v_alt; }; @@ -448,9 +422,9 @@ struct __pyx_obj_6ctabix_asVCF { * * cdef: */ -struct __pyx_obj_10TabProxies_TupleProxy { +struct __pyx_obj_5pysam_10TabProxies_TupleProxy { PyObject_HEAD - struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab; + struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab; char *data; char **fields; int nfields; @@ -468,8 +442,8 @@ struct __pyx_obj_10TabProxies_TupleProxy { * pass * */ -struct __pyx_obj_10TabProxies_NamedTupleProxy { - struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; +struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy { + struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; }; @@ -480,8 +454,8 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy { * * cdef: */ -struct __pyx_obj_10TabProxies_BedProxy { - struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base; +struct __pyx_obj_5pysam_10TabProxies_BedProxy { + struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t start; uint32_t end; @@ -489,58 +463,91 @@ struct __pyx_obj_10TabProxies_BedProxy { }; -/* "ctabix.pxd":218 - * cdef __cnext__(self) +/* "ctabix.pxd":186 + * cdef tabix_t * tabixfile * - * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef Parser parser + * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile */ -struct __pyx_obj_6ctabix_tabix_copy_iterator { +struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator { PyObject_HEAD - struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab; - FILE *infile; - struct __pyx_obj_6ctabix_Parser *parser; + ti_iter_t iterator; + tabix_t *tabixfile; }; -/* "cvcf.pyx":94 - * ########################################################################################################### - * - * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< - * '''vcf record. +/* "ctabix.pxd":205 + * pass * + * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile */ -struct __pyx_obj_4cvcf_VCFRecord { - struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; - PyObject *vcf; - char *contig; - uint32_t pos; +struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed { + PyObject_HEAD + ti_iter_t iterator; + tabix_t *tabixfile; + struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; -/* "TabProxies.pxd":83 - * cdef update( self, char * buffer, size_t nbytes ) +/* "ctabix.pxd":182 + * cdef char * _filename * - * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< + * cdef class TabixIterator: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile + */ +struct __pyx_obj_5pysam_6ctabix_TabixIterator { + PyObject_HEAD + ti_iter_t iterator; + tabix_t *tabixfile; +}; + + +/* "ctabix.pxd":210 + * cdef Parser parser * - * cdef: + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef char * buffer */ -struct __pyx_obj_10TabProxies_VCFProxy { - struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base; - char *contig; - uint32_t pos; +struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator { + PyObject_HEAD + struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab; + FILE *infile; + char *buffer; + size_t size; + struct __pyx_obj_5pysam_6ctabix_Parser *parser; +}; + + +/* "pysam/cvcf.pyx":790 + * if alt: + * for i in range(1,min(len(ref),min(map(len,alt)))): + * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<< + * break + * ref, alt = ref[:-1], [allele[:-1] for allele in alt] + */ +struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr { + PyObject_HEAD + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope; + PyObject *__pyx_v_allele; + PyObject *__pyx_t_0; + Py_ssize_t __pyx_t_1; + PyObject *(*__pyx_t_2)(PyObject *); }; -/* "cvcf.pyx":899 +/* "pysam/cvcf.pyx":899 * return line * * def _parse(self, line, stream): # <<<<<<<<<<<<<< * # deal with files with header only * if line.startswith("##"): return */ -struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse { +struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse { PyObject_HEAD PyObject *__pyx_v_d; PyObject *__pyx_v_line; @@ -552,89 +559,46 @@ struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse { }; -/* "cvcf.pyx":647 - * return False +/* "ctabix.pxd":218 + * cdef __cnext__(self) * - * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< - * cols = line.split('\t') - * if len(cols) != len(self._samples)+9: + * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef Parser parser */ -struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data { +struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator { PyObject_HEAD - PyObject *__pyx_v_alt; + struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab; + FILE *infile; + struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; -/* "ctabix.pxd":182 - * cdef char * _filename - * - * cdef class TabixIterator: # <<<<<<<<<<<<<< - * cdef ti_iter_t iterator +/* "ctabix.pxd":190 * cdef tabix_t * tabixfile + * + * cdef class Parser: # <<<<<<<<<<<<<< + * pass + * */ -struct __pyx_obj_6ctabix_TabixIterator { +struct __pyx_obj_5pysam_6ctabix_Parser { PyObject_HEAD - ti_iter_t iterator; - tabix_t *tabixfile; }; -/* "cvcf.pyx":226 +/* "pysam/cvcf.pyx":226 * * * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<< * '''converts a :term:`tabix row` into a VCF record.''' * cdef vcffile */ -struct __pyx_obj_4cvcf_asVCFRecord { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_5pysam_4cvcf_asVCFRecord { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; PyObject *vcffile; }; -/* "TabProxies.pxd":60 - * cdef update( self, char * buffer, size_t nbytes ) - * - * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< - * - * cdef: - */ -struct __pyx_obj_10TabProxies_GTFProxy { - struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; - char *_attributes; - int hasOwnAttributes; -}; - - -/* "ctabix.pxd":205 - * pass - * - * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< - * cdef ti_iter_t iterator - * cdef tabix_t * tabixfile - */ -struct __pyx_obj_6ctabix_TabixIteratorParsed { - PyObject_HEAD - ti_iter_t iterator; - tabix_t *tabixfile; - struct __pyx_obj_6ctabix_Parser *parser; -}; - - -/* "ctabix.pxd":186 - * cdef tabix_t * tabixfile - * - * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< - * cdef ti_iter_t iterator - * cdef tabix_t * tabixfile - */ -struct __pyx_obj_6ctabix_TabixHeaderIterator { - PyObject_HEAD - ti_iter_t iterator; - tabix_t *tabixfile; -}; - - /* "ctabix.pxd":172 * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) * @@ -642,7 +606,7 @@ struct __pyx_obj_6ctabix_TabixHeaderIterator { * * # pointer to tabixfile */ -struct __pyx_obj_6ctabix_Tabixfile { +struct __pyx_obj_5pysam_6ctabix_Tabixfile { PyObject_HEAD tabix_t *tabixfile; int isremote; @@ -650,61 +614,56 @@ struct __pyx_obj_6ctabix_Tabixfile { }; -/* "ctabix.pxd":196 +/* "ctabix.pxd":199 * pass * - * cdef class asGTF(Parser): # <<<<<<<<<<<<<< + * cdef class asBed(Parser): # <<<<<<<<<<<<<< * pass * */ -struct __pyx_obj_6ctabix_asGTF { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_5pysam_6ctabix_asBed { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; -/* "ctabix.pxd":199 +/* "ctabix.pxd":196 * pass * - * cdef class asBed(Parser): # <<<<<<<<<<<<<< + * cdef class asGTF(Parser): # <<<<<<<<<<<<<< * pass * */ -struct __pyx_obj_6ctabix_asBed { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_5pysam_6ctabix_asGTF { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; -/* "ctabix.pxd":210 - * cdef Parser parser +/* "TabProxies.pxd":83 + * cdef update( self, char * buffer, size_t nbytes ) * - * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef char * buffer + * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< + * + * cdef: */ -struct __pyx_obj_6ctabix_tabix_inplace_iterator { - PyObject_HEAD - struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab; - FILE *infile; - char *buffer; - size_t size; - struct __pyx_obj_6ctabix_Parser *parser; +struct __pyx_obj_5pysam_10TabProxies_VCFProxy { + struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; + char *contig; + uint32_t pos; }; -/* "cvcf.pyx":790 - * if alt: - * for i in range(1,min(len(ref),min(map(len,alt)))): - * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<< - * break - * ref, alt = ref[:-1], [allele[:-1] for allele in alt] +/* "pysam/cvcf.pyx":94 + * ########################################################################################################### + * + * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< + * '''vcf record. + * */ -struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr { - PyObject_HEAD - struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope; - PyObject *__pyx_v_allele; - PyObject *__pyx_t_0; - Py_ssize_t __pyx_t_1; - PyObject *(*__pyx_t_2)(PyObject *); +struct __pyx_obj_5pysam_4cvcf_VCFRecord { + struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; + PyObject *vcf; + char *contig; + uint32_t pos; }; @@ -715,24 +674,36 @@ struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr { * pass * */ -struct __pyx_obj_6ctabix_asTuple { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_5pysam_6ctabix_asTuple { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; - -/* "ctabix.pxd":218 - * cdef __cnext__(self) +/* "TabProxies.pxd":60 + * cdef update( self, char * buffer, size_t nbytes ) * - * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef Parser parser + * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< + * + * cdef: */ +struct __pyx_obj_5pysam_10TabProxies_GTFProxy { + struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; + char *_attributes; + int hasOwnAttributes; +}; + -struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator { - PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *); +/* "ctabix.pxd":202 + * pass + * + * cdef class asVCF(Parser): # <<<<<<<<<<<<<< + * pass + * + */ +struct __pyx_obj_5pysam_6ctabix_asVCF { + struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; -static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator; + /* "TabProxies.pxd":41 @@ -743,14 +714,14 @@ static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabi * cdef: */ -struct __pyx_vtabstruct_10TabProxies_TupleProxy { - int (*getMaxFields)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t); - PyObject *(*take)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); - PyObject *(*present)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); - PyObject *(*copy)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); - PyObject *(*update)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t); +struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy { + int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t); + PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); + PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); + PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); + PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); }; -static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy; /* "TabProxies.pxd":69 @@ -761,10 +732,10 @@ static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxi * */ -struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy { - struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base; +struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy; /* "TabProxies.pxd":83 @@ -775,24 +746,38 @@ static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10Tab * cdef: */ -struct __pyx_vtabstruct_10TabProxies_VCFProxy { - struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; +struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy; -/* "ctabix.pxd":210 - * cdef Parser parser +/* "pysam/cvcf.pyx":94 + * ########################################################################################################### * - * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef char * buffer + * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< + * '''vcf record. + * + */ + +struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord { + struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; +}; +static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord; + + +/* "ctabix.pxd":210 + * cdef Parser parser + * + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef char * buffer */ -struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator { - PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *); +struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *); }; -static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator; +static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator; /* "TabProxies.pxd":60 @@ -803,25 +788,25 @@ static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ct * cdef: */ -struct __pyx_vtabstruct_10TabProxies_GTFProxy { - struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base; - char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *); +struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; + char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *); }; -static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy; -/* "cvcf.pyx":94 - * ########################################################################################################### - * - * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< - * '''vcf record. +/* "ctabix.pxd":218 + * cdef __cnext__(self) * + * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef Parser parser */ -struct __pyx_vtabstruct_4cvcf_VCFRecord { - struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base; +struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *); }; -static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord; +static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator; /* "TabProxies.pxd":72 @@ -832,10 +817,10 @@ static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord; * cdef: */ -struct __pyx_vtabstruct_10TabProxies_BedProxy { - struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; +struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy { + struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy; +static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy; #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -912,42 +897,47 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j __Pyx_GetItemInt_List_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { - if (likely(o != Py_None)) { - if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, i); - Py_INCREF(r); - return r; - } - else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) { - PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i); - Py_INCREF(r); - return r; - } +#if CYTHON_COMPILING_IN_CPYTHON + if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i); + Py_INCREF(r); + return r; } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif } #define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_Tuple_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { - if (likely(o != Py_None)) { - if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, i); - Py_INCREF(r); - return r; - } - else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) { - PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i); - Py_INCREF(r); - return r; - } +#if CYTHON_COMPILING_IN_CPYTHON + if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i); + Py_INCREF(r); + return r; } return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif } #define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) { +#if CYTHON_COMPILING_IN_CPYTHON if (PyList_CheckExact(o)) { Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { @@ -963,13 +953,22 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) Py_INCREF(r); return r; } - } - else if (likely(i >= 0)) { + } else { /* inlined PySequence_GetItem() */ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; if (likely(m && m->sq_item)) { + if (unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (unlikely(l < 0)) return NULL; + i += l; + } return m->sq_item(o, i); } } +#else + if (PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } @@ -981,21 +980,22 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ +#if CYTHON_COMPILING_IN_PYPY +#define __Pyx_PyObject_AsDouble(obj) \ +(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \ + likely(PyInt_CheckExact(obj)) ? \ + PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj)) +#else #define __Pyx_PyObject_AsDouble(obj) \ ((likely(PyFloat_CheckExact(obj))) ? \ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) +#endif static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); -static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void); - #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; - if (unlikely(d == Py_None)) { - __Pyx_RaiseNoneIndexingError(); - return NULL; - } value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (!PyErr_Occurred()) @@ -1009,28 +1009,48 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif -static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) { - return unlikely(b < 0) ? b : !b; -} -static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { - return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b); +static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) { + int result = PySequence_Contains(seq, item); + return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); +static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ +static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) { + int result = PyDict_Contains(dict, item); + return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { if (likely(PyList_CheckExact(L))) { - if (PyList_Append(L, x) < 0) return NULL; + if (unlikely(PyList_Append(L, x) < 0)) return NULL; Py_INCREF(Py_None); return Py_None; /* this is just to have an accurate signature */ - } - else { + } else { PyObject *r, *m; m = __Pyx_GetAttrString(L, "append"); if (!m) return NULL; @@ -1040,6 +1060,18 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { } } +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/ + +static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2, + int is_tuple, int has_known_size, int decref_tuple); + +static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name, + Py_ssize_t* p_orig_length, int* p_is_dict); +static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos, + PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict); + #define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_SetItemInt_Fast(o, i, v) : \ __Pyx_SetItemInt_Generic(o, to_py_func(i), v)) @@ -1051,6 +1083,7 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyOb return r; } static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) { +#if CYTHON_COMPILING_IN_CPYTHON if (PyList_CheckExact(o)) { Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { @@ -1060,13 +1093,26 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje Py_DECREF(old); return 1; } - } - else if (likely(i >= 0)) { + } else { /* inlined PySequence_SetItem() */ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; if (likely(m && m->sq_ass_item)) { + if (unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (unlikely(l < 0)) return -1; + i += l; + } return m->sq_ass_item(o, i, v); } } +#else +#if CYTHON_COMPILING_IN_PYPY + if (PySequence_Check(o) && !PyDict_Check(o)) { +#else + if (PySequence_Check(o)) { +#endif + return PySequence_SetItem(o, i, v); + } +#endif return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); } @@ -1105,6 +1151,12 @@ static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) { #endif /* PyAnySet_CheckExact (<= Py2.4) */ #endif /* < Py2.5 */ +static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc); + +static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); + +static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc); + static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ @@ -1161,18 +1213,6 @@ static int __Pyx_CyFunction_init(void); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); -#include - -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ - -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ - -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals -#else -#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals -#endif - static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); @@ -1209,22 +1249,30 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, #define __Pyx_Generator_USED #include +#include typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); typedef struct { PyObject_HEAD __pyx_generator_body_t body; PyObject *closure; - int is_running; - int resume_label; PyObject *exc_type; PyObject *exc_value; PyObject *exc_traceback; PyObject *gi_weakreflist; PyObject *classobj; + PyObject *yieldfrom; + int resume_label; + char is_running; // using T_BOOL for property below requires char value } __pyx_GeneratorObject; static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject *closure); static int __pyx_Generator_init(void); +static int __Pyx_Generator_clear(PyObject* self); +#if 1 || PY_VERSION_HEX < 0x030300B0 +static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue); +#else +#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue) +#endif static int __Pyx_check_binary_version(void); @@ -1236,10 +1284,10 @@ static int __Pyx_check_binary_version(void); #endif #endif -static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ - static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ + static void* __Pyx_GetVtable(PyObject *dict); /*proto*/ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ @@ -1264,36 +1312,38 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ -/* Module declarations from 'ctabix' */ -static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0; -static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0; -static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 0; -static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asTuple = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asGTF = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asBed = 0; -static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0; -static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0; -static PyTypeObject *__pyx_ptype_6ctabix_tabix_inplace_iterator = 0; -static PyTypeObject *__pyx_ptype_6ctabix_tabix_copy_iterator = 0; - -/* Module declarations from 'TabProxies' */ -static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0; -static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0; - -/* Module declarations from 'cvcf' */ -static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0; -static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0; -static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct__parse_data = 0; -static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr = 0; -static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct_2__parse = 0; -#define __Pyx_MODULE_NAME "cvcf" -int __pyx_module_is_main_cvcf = 0; - -/* Implementation of 'cvcf' */ +/* Module declarations from 'pysam' */ + +/* Module declarations from 'pysam.ctabix' */ +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Parser = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = 0; +static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = 0; + +/* Module declarations from 'pysam.TabProxies' */ +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0; +static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0; + +/* Module declarations from 'pysam.cvcf' */ +static PyTypeObject *__pyx_ptype_5pysam_4cvcf_VCFRecord = 0; +static PyTypeObject *__pyx_ptype_5pysam_4cvcf_asVCFRecord = 0; +static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data = 0; +static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr = 0; +static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = 0; +#define __Pyx_MODULE_NAME "pysam.cvcf" +int __pyx_module_is_main_pysam__cvcf = 0; + +/* Implementation of 'pysam.cvcf' */ static PyObject *__pyx_builtin_object; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; @@ -1304,73 +1354,73 @@ static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_NotImplementedError; -static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */ -static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */ -static int __pyx_pf_4cvcf_9VCFRecord___init__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ -static int __pyx_pf_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ -static Py_ssize_t __pyx_pf_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ -static int __pyx_pf_4cvcf_11asVCFRecord___init__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */ -static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ -static PyObject *__pyx_pf_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */ +static int __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ +static int __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ +static Py_ssize_t __pyx_pf_5pysam_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static int __pyx_pf_5pysam_4cvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */ static char __pyx_k_1[] = ""; static char __pyx_k_2[] = ","; static char __pyx_k_4[] = ":"; @@ -1469,41 +1519,42 @@ static char __pyx_k_126[] = "needs to be checked"; static char __pyx_k_128[] = "[|/\\\\]"; static char __pyx_k_130[] = "^[ACGTN]+$"; static char __pyx_k_134[] = "/ifs/devel/pysam/pysam/cvcf.pyx"; -static char __pyx_k_137[] = "id numbertype number type description missingvalue"; -static char __pyx_k_139[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier"; -static char __pyx_k_140[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string"; -static char __pyx_k_141[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s"; -static char __pyx_k_142[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)"; -static char __pyx_k_143[] = "POS_NOT_NUMERICAL:Position column is not numerical"; -static char __pyx_k_144[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field"; -static char __pyx_k_145[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF"; -static char __pyx_k_146[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF"; -static char __pyx_k_147[] = "POS_NOT_POSITIVE:Position field must be >0"; -static char __pyx_k_148[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'"; -static char __pyx_k_149[] = "ERROR_INFO_STRING:Error while parsing info field"; -static char __pyx_k_150[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)"; -static char __pyx_k_151[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s"; -static char __pyx_k_152[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string"; -static char __pyx_k_153[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header"; -static char __pyx_k_154[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header"; -static char __pyx_k_155[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)"; -static char __pyx_k_156[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)"; -static char __pyx_k_157[] = "BAD_GENOTYPE:Cannot parse genotype (%s)"; -static char __pyx_k_158[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)"; -static char __pyx_k_159[] = "MISSING_REF:Reference allele missing"; -static char __pyx_k_160[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)"; -static char __pyx_k_161[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets"; -static char __pyx_k_162[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes"; -static char __pyx_k_163[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields"; -static char __pyx_k_164[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs"; -static char __pyx_k_165[] = "WRONG_REF:Wrong reference %s"; -static char __pyx_k_166[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data"; -static char __pyx_k_167[] = "BAD_CHR_TAG:Error calculating chr tag for %s"; -static char __pyx_k_168[] = "ZERO_LENGTH_ALLELE:Found zero-length allele"; -static char __pyx_k_169[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"; -static char __pyx_k_170[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'"; -static char __pyx_k_171[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s"; -static char __pyx_k_172[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value"; +static char __pyx_k_135[] = "pysam.cvcf"; +static char __pyx_k_138[] = "id numbertype number type description missingvalue"; +static char __pyx_k_140[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier"; +static char __pyx_k_141[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string"; +static char __pyx_k_142[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s"; +static char __pyx_k_143[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)"; +static char __pyx_k_144[] = "POS_NOT_NUMERICAL:Position column is not numerical"; +static char __pyx_k_145[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field"; +static char __pyx_k_146[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF"; +static char __pyx_k_147[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF"; +static char __pyx_k_148[] = "POS_NOT_POSITIVE:Position field must be >0"; +static char __pyx_k_149[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'"; +static char __pyx_k_150[] = "ERROR_INFO_STRING:Error while parsing info field"; +static char __pyx_k_151[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)"; +static char __pyx_k_152[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s"; +static char __pyx_k_153[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string"; +static char __pyx_k_154[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header"; +static char __pyx_k_155[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header"; +static char __pyx_k_156[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)"; +static char __pyx_k_157[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)"; +static char __pyx_k_158[] = "BAD_GENOTYPE:Cannot parse genotype (%s)"; +static char __pyx_k_159[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)"; +static char __pyx_k_160[] = "MISSING_REF:Reference allele missing"; +static char __pyx_k_161[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)"; +static char __pyx_k_162[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets"; +static char __pyx_k_163[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes"; +static char __pyx_k_164[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields"; +static char __pyx_k_165[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs"; +static char __pyx_k_166[] = "WRONG_REF:Wrong reference %s"; +static char __pyx_k_167[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data"; +static char __pyx_k_168[] = "BAD_CHR_TAG:Error calculating chr tag for %s"; +static char __pyx_k_169[] = "ZERO_LENGTH_ALLELE:Found zero-length allele"; +static char __pyx_k_170[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"; +static char __pyx_k_171[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'"; +static char __pyx_k_172[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s"; +static char __pyx_k_173[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value"; static char __pyx_k__DP[] = "DP"; static char __pyx_k__EC[] = "EC"; static char __pyx_k__FT[] = "FT"; @@ -1556,7 +1607,6 @@ static char __pyx_k__alt1[] = "alt1"; static char __pyx_k__alt2[] = "alt2"; static char __pyx_k__cols[] = "cols"; static char __pyx_k__copy[] = "copy"; -static char __pyx_k__cvcf[] = "cvcf"; static char __pyx_k__data[] = "data"; static char __pyx_k__dict[] = "dict"; static char __pyx_k__elts[] = "elts"; @@ -1783,8 +1833,8 @@ static PyObject *__pyx_kp_s_126; static PyObject *__pyx_kp_s_128; static PyObject *__pyx_kp_s_130; static PyObject *__pyx_kp_s_134; -static PyObject *__pyx_kp_s_137; -static PyObject *__pyx_kp_s_139; +static PyObject *__pyx_n_s_135; +static PyObject *__pyx_kp_s_138; static PyObject *__pyx_kp_s_14; static PyObject *__pyx_kp_s_140; static PyObject *__pyx_kp_s_141; @@ -1819,6 +1869,7 @@ static PyObject *__pyx_kp_s_169; static PyObject *__pyx_kp_s_170; static PyObject *__pyx_kp_s_171; static PyObject *__pyx_kp_s_172; +static PyObject *__pyx_kp_s_173; static PyObject *__pyx_n_s_18; static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_2; @@ -2000,7 +2051,6 @@ static PyObject *__pyx_n_s__connect; static PyObject *__pyx_n_s__convertGT; static PyObject *__pyx_n_s__convertGTback; static PyObject *__pyx_n_s__copy; -static PyObject *__pyx_n_s__cvcf; static PyObject *__pyx_n_s__d; static PyObject *__pyx_n_s__data; static PyObject *__pyx_n_s__datagenerator; @@ -2253,111 +2303,110 @@ static PyObject *__pyx_k_tuple_127; static PyObject *__pyx_k_tuple_129; static PyObject *__pyx_k_tuple_131; static PyObject *__pyx_k_tuple_132; -static PyObject *__pyx_k_tuple_135; -static PyObject *__pyx_k_tuple_138; -static PyObject *__pyx_k_tuple_173; -static PyObject *__pyx_k_tuple_175; -static PyObject *__pyx_k_tuple_177; +static PyObject *__pyx_k_tuple_136; +static PyObject *__pyx_k_tuple_139; +static PyObject *__pyx_k_tuple_174; +static PyObject *__pyx_k_tuple_176; static PyObject *__pyx_k_tuple_178; -static PyObject *__pyx_k_tuple_180; -static PyObject *__pyx_k_tuple_182; -static PyObject *__pyx_k_tuple_184; -static PyObject *__pyx_k_tuple_186; -static PyObject *__pyx_k_tuple_188; -static PyObject *__pyx_k_tuple_190; -static PyObject *__pyx_k_tuple_192; -static PyObject *__pyx_k_tuple_194; -static PyObject *__pyx_k_tuple_196; -static PyObject *__pyx_k_tuple_198; -static PyObject *__pyx_k_tuple_200; -static PyObject *__pyx_k_tuple_202; -static PyObject *__pyx_k_tuple_204; -static PyObject *__pyx_k_tuple_206; -static PyObject *__pyx_k_tuple_208; -static PyObject *__pyx_k_tuple_210; -static PyObject *__pyx_k_tuple_212; -static PyObject *__pyx_k_tuple_214; -static PyObject *__pyx_k_tuple_216; -static PyObject *__pyx_k_tuple_218; -static PyObject *__pyx_k_tuple_220; -static PyObject *__pyx_k_tuple_222; -static PyObject *__pyx_k_tuple_224; -static PyObject *__pyx_k_tuple_226; -static PyObject *__pyx_k_tuple_228; -static PyObject *__pyx_k_tuple_230; -static PyObject *__pyx_k_tuple_232; -static PyObject *__pyx_k_tuple_234; -static PyObject *__pyx_k_tuple_236; -static PyObject *__pyx_k_tuple_238; -static PyObject *__pyx_k_tuple_240; -static PyObject *__pyx_k_tuple_242; -static PyObject *__pyx_k_tuple_244; -static PyObject *__pyx_k_tuple_246; -static PyObject *__pyx_k_tuple_248; -static PyObject *__pyx_k_tuple_250; -static PyObject *__pyx_k_tuple_252; -static PyObject *__pyx_k_tuple_254; -static PyObject *__pyx_k_tuple_256; +static PyObject *__pyx_k_tuple_179; +static PyObject *__pyx_k_tuple_181; +static PyObject *__pyx_k_tuple_183; +static PyObject *__pyx_k_tuple_185; +static PyObject *__pyx_k_tuple_187; +static PyObject *__pyx_k_tuple_189; +static PyObject *__pyx_k_tuple_191; +static PyObject *__pyx_k_tuple_193; +static PyObject *__pyx_k_tuple_195; +static PyObject *__pyx_k_tuple_197; +static PyObject *__pyx_k_tuple_199; +static PyObject *__pyx_k_tuple_201; +static PyObject *__pyx_k_tuple_203; +static PyObject *__pyx_k_tuple_205; +static PyObject *__pyx_k_tuple_207; +static PyObject *__pyx_k_tuple_209; +static PyObject *__pyx_k_tuple_211; +static PyObject *__pyx_k_tuple_213; +static PyObject *__pyx_k_tuple_215; +static PyObject *__pyx_k_tuple_217; +static PyObject *__pyx_k_tuple_219; +static PyObject *__pyx_k_tuple_221; +static PyObject *__pyx_k_tuple_223; +static PyObject *__pyx_k_tuple_225; +static PyObject *__pyx_k_tuple_227; +static PyObject *__pyx_k_tuple_229; +static PyObject *__pyx_k_tuple_231; +static PyObject *__pyx_k_tuple_233; +static PyObject *__pyx_k_tuple_235; +static PyObject *__pyx_k_tuple_237; +static PyObject *__pyx_k_tuple_239; +static PyObject *__pyx_k_tuple_241; +static PyObject *__pyx_k_tuple_243; +static PyObject *__pyx_k_tuple_245; +static PyObject *__pyx_k_tuple_247; +static PyObject *__pyx_k_tuple_249; +static PyObject *__pyx_k_tuple_251; +static PyObject *__pyx_k_tuple_253; +static PyObject *__pyx_k_tuple_255; static PyObject *__pyx_k_tuple_257; +static PyObject *__pyx_k_tuple_258; static PyObject *__pyx_k_codeobj_133; -static PyObject *__pyx_k_codeobj_136; -static PyObject *__pyx_k_codeobj_174; -static PyObject *__pyx_k_codeobj_176; -static PyObject *__pyx_k_codeobj_179; -static PyObject *__pyx_k_codeobj_181; -static PyObject *__pyx_k_codeobj_183; -static PyObject *__pyx_k_codeobj_185; -static PyObject *__pyx_k_codeobj_187; -static PyObject *__pyx_k_codeobj_189; -static PyObject *__pyx_k_codeobj_191; -static PyObject *__pyx_k_codeobj_193; -static PyObject *__pyx_k_codeobj_195; -static PyObject *__pyx_k_codeobj_197; -static PyObject *__pyx_k_codeobj_199; -static PyObject *__pyx_k_codeobj_201; -static PyObject *__pyx_k_codeobj_203; -static PyObject *__pyx_k_codeobj_205; -static PyObject *__pyx_k_codeobj_207; -static PyObject *__pyx_k_codeobj_209; -static PyObject *__pyx_k_codeobj_211; -static PyObject *__pyx_k_codeobj_213; -static PyObject *__pyx_k_codeobj_215; -static PyObject *__pyx_k_codeobj_217; -static PyObject *__pyx_k_codeobj_219; -static PyObject *__pyx_k_codeobj_221; -static PyObject *__pyx_k_codeobj_223; -static PyObject *__pyx_k_codeobj_225; -static PyObject *__pyx_k_codeobj_227; -static PyObject *__pyx_k_codeobj_229; -static PyObject *__pyx_k_codeobj_231; -static PyObject *__pyx_k_codeobj_233; -static PyObject *__pyx_k_codeobj_235; -static PyObject *__pyx_k_codeobj_237; -static PyObject *__pyx_k_codeobj_239; -static PyObject *__pyx_k_codeobj_241; -static PyObject *__pyx_k_codeobj_243; -static PyObject *__pyx_k_codeobj_245; -static PyObject *__pyx_k_codeobj_247; -static PyObject *__pyx_k_codeobj_249; -static PyObject *__pyx_k_codeobj_251; -static PyObject *__pyx_k_codeobj_253; -static PyObject *__pyx_k_codeobj_255; -static PyObject *__pyx_k_codeobj_258; +static PyObject *__pyx_k_codeobj_137; +static PyObject *__pyx_k_codeobj_175; +static PyObject *__pyx_k_codeobj_177; +static PyObject *__pyx_k_codeobj_180; +static PyObject *__pyx_k_codeobj_182; +static PyObject *__pyx_k_codeobj_184; +static PyObject *__pyx_k_codeobj_186; +static PyObject *__pyx_k_codeobj_188; +static PyObject *__pyx_k_codeobj_190; +static PyObject *__pyx_k_codeobj_192; +static PyObject *__pyx_k_codeobj_194; +static PyObject *__pyx_k_codeobj_196; +static PyObject *__pyx_k_codeobj_198; +static PyObject *__pyx_k_codeobj_200; +static PyObject *__pyx_k_codeobj_202; +static PyObject *__pyx_k_codeobj_204; +static PyObject *__pyx_k_codeobj_206; +static PyObject *__pyx_k_codeobj_208; +static PyObject *__pyx_k_codeobj_210; +static PyObject *__pyx_k_codeobj_212; +static PyObject *__pyx_k_codeobj_214; +static PyObject *__pyx_k_codeobj_216; +static PyObject *__pyx_k_codeobj_218; +static PyObject *__pyx_k_codeobj_220; +static PyObject *__pyx_k_codeobj_222; +static PyObject *__pyx_k_codeobj_224; +static PyObject *__pyx_k_codeobj_226; +static PyObject *__pyx_k_codeobj_228; +static PyObject *__pyx_k_codeobj_230; +static PyObject *__pyx_k_codeobj_232; +static PyObject *__pyx_k_codeobj_234; +static PyObject *__pyx_k_codeobj_236; +static PyObject *__pyx_k_codeobj_238; +static PyObject *__pyx_k_codeobj_240; +static PyObject *__pyx_k_codeobj_242; +static PyObject *__pyx_k_codeobj_244; +static PyObject *__pyx_k_codeobj_246; +static PyObject *__pyx_k_codeobj_248; +static PyObject *__pyx_k_codeobj_250; +static PyObject *__pyx_k_codeobj_252; +static PyObject *__pyx_k_codeobj_254; +static PyObject *__pyx_k_codeobj_256; +static PyObject *__pyx_k_codeobj_259; /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_1get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pw_4cvcf_1get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_1get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pw_5pysam_4cvcf_1get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_chrom = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_fa = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("get_sequence (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0}; PyObject* values[4] = {0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -2373,24 +2422,20 @@ static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa); - if (likely(values[3])) kw_args--; + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -2415,16 +2460,16 @@ static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.get_sequence", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.get_sequence", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_get_sequence(__pyx_self, __pyx_v_chrom, __pyx_v_start, __pyx_v_end, __pyx_v_fa); + __pyx_r = __pyx_pf_5pysam_4cvcf_get_sequence(__pyx_self, __pyx_v_chrom, __pyx_v_start, __pyx_v_end, __pyx_v_fa); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":58 +/* "pysam/cvcf.pyx":58 * * # Utility function. Uses 0-based coordinates * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<< @@ -2432,7 +2477,7 @@ static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__ * if end<=start: return "" */ -static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa) { +static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa) { PyObject *__pyx_v_sequence = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -2448,15 +2493,14 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_sequence", 0); - /* "cvcf.pyx":60 + /* "pysam/cvcf.pyx":60 * def get_sequence(chrom, start, end, fa): * # obtain sequence from .fa file, without truncation * if end<=start: return "" # <<<<<<<<<<<<<< * if not fa: return "N"*(end-start) * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { @@ -2468,7 +2512,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_L3:; - /* "cvcf.pyx":61 + /* "pysam/cvcf.pyx":61 * # obtain sequence from .fa file, without truncation * if end<=start: return "" * if not fa: return "N"*(end-start) # <<<<<<<<<<<<<< @@ -2491,15 +2535,14 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_L4:; - /* "cvcf.pyx":62 + /* "pysam/cvcf.pyx":62 * if end<=start: return "" * if not fa: return "N"*(end-start) * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() # <<<<<<<<<<<<<< * sequence = fa.fetch(chrom, start, end).upper() * if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) */ - __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_3) { @@ -2546,7 +2589,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_L5:; - /* "cvcf.pyx":63 + /* "pysam/cvcf.pyx":63 * if not fa: return "N"*(end-start) * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() * sequence = fa.fetch(chrom, start, end).upper() # <<<<<<<<<<<<<< @@ -2579,7 +2622,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, __pyx_v_sequence = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":64 + /* "pysam/cvcf.pyx":64 * if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() * sequence = fa.fetch(chrom, start, end).upper() * if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) # <<<<<<<<<<<<<< @@ -2591,8 +2634,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_GOTREF(__pyx_t_1); __pyx_t_6 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -2620,7 +2662,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_L6:; - /* "cvcf.pyx":65 + /* "pysam/cvcf.pyx":65 * sequence = fa.fetch(chrom, start, end).upper() * if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) * return sequence # <<<<<<<<<<<<<< @@ -2639,7 +2681,7 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("cvcf.get_sequence", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.get_sequence", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_sequence); @@ -2649,19 +2691,18 @@ static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3parse_regions = {__Pyx_NAMESTR("parse_regions"), (PyCFunction)__pyx_pw_4cvcf_3parse_regions, METH_O, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string) { +static PyObject *__pyx_pw_5pysam_4cvcf_3parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3parse_regions = {__Pyx_NAMESTR("parse_regions"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3parse_regions, METH_O, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3parse_regions(PyObject *__pyx_self, PyObject *__pyx_v_string) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("parse_regions (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_4cvcf_2parse_regions(__pyx_self, ((PyObject *)__pyx_v_string)); + __pyx_r = __pyx_pf_5pysam_4cvcf_2parse_regions(__pyx_self, ((PyObject *)__pyx_v_string)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":68 +/* "pysam/cvcf.pyx":68 * * # Utility function. Parses a region string * def parse_regions( string ): # <<<<<<<<<<<<<< @@ -2669,7 +2710,7 @@ static PyObject *__pyx_pw_4cvcf_3parse_regions(PyObject *__pyx_self, PyObject *_ * for r in string.split(','): */ -static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string) { +static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string) { PyObject *__pyx_v_result = NULL; PyObject *__pyx_v_r = NULL; PyObject *__pyx_v_elts = NULL; @@ -2698,7 +2739,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel int __pyx_clineno = 0; __Pyx_RefNannySetupContext("parse_regions", 0); - /* "cvcf.pyx":69 + /* "pysam/cvcf.pyx":69 * # Utility function. Parses a region string * def parse_regions( string ): * result = [] # <<<<<<<<<<<<<< @@ -2710,7 +2751,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __pyx_v_result = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":70 + /* "pysam/cvcf.pyx":70 * def parse_regions( string ): * result = [] * for r in string.split(','): # <<<<<<<<<<<<<< @@ -2734,10 +2775,18 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel for (;;) { if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_2 = __pyx_t_4(__pyx_t_1); if (unlikely(!__pyx_t_2)) { @@ -2753,7 +2802,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __pyx_v_r = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":71 + /* "pysam/cvcf.pyx":71 * result = [] * for r in string.split(','): * elts = r.split(':') # <<<<<<<<<<<<<< @@ -2769,7 +2818,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __pyx_v_elts = __pyx_t_5; __pyx_t_5 = 0; - /* "cvcf.pyx":72 + /* "pysam/cvcf.pyx":72 * for r in string.split(','): * elts = r.split(':') * chrom, start, end = elts[0], 0, 3000000000 # <<<<<<<<<<<<<< @@ -2792,7 +2841,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __pyx_v_end = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":73 + /* "pysam/cvcf.pyx":73 * elts = r.split(':') * chrom, start, end = elts[0], 0, 3000000000 * if len(elts)==1: pass # <<<<<<<<<<<<<< @@ -2805,7 +2854,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel goto __pyx_L5; } - /* "cvcf.pyx":74 + /* "pysam/cvcf.pyx":74 * chrom, start, end = elts[0], 0, 3000000000 * if len(elts)==1: pass * elif len(elts)==2: # <<<<<<<<<<<<<< @@ -2816,7 +2865,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __pyx_t_8 = (__pyx_t_7 == 2); if (__pyx_t_8) { - /* "cvcf.pyx":75 + /* "pysam/cvcf.pyx":75 * if len(elts)==1: pass * elif len(elts)==2: * if len(elts[1])>0: # <<<<<<<<<<<<<< @@ -2830,7 +2879,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __pyx_t_8 = (__pyx_t_7 > 0); if (__pyx_t_8) { - /* "cvcf.pyx":76 + /* "pysam/cvcf.pyx":76 * elif len(elts)==2: * if len(elts[1])>0: * ielts = elts[1].split('-') # <<<<<<<<<<<<<< @@ -2849,7 +2898,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __pyx_v_ielts = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":77 + /* "pysam/cvcf.pyx":77 * if len(elts[1])>0: * ielts = elts[1].split('-') * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<< @@ -2874,7 +2923,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L7:; - /* "cvcf.pyx":78 + /* "pysam/cvcf.pyx":78 * ielts = elts[1].split('-') * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) * try: start, end = int(ielts[0])-1, int(ielts[1]) # <<<<<<<<<<<<<< @@ -2926,7 +2975,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "cvcf.pyx":79 + /* "pysam/cvcf.pyx":79 * if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) * try: start, end = int(ielts[0])-1, int(ielts[1]) * except: raise ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<< @@ -2934,7 +2983,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel * raise ValueError("Don't understand region string '%s'" % r) */ /*except:*/ { - __Pyx_AddTraceback("cvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_2, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_2); @@ -2977,7 +3026,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel } /*else*/ { - /* "cvcf.pyx":81 + /* "pysam/cvcf.pyx":81 * except: raise ValueError("Don't understand region string '%s'" % r) * else: * raise ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<< @@ -3000,7 +3049,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel } __pyx_L5:; - /* "cvcf.pyx":82 + /* "pysam/cvcf.pyx":82 * else: * raise ValueError("Don't understand region string '%s'" % r) * result.append( (chrom,start,end) ) # <<<<<<<<<<<<<< @@ -3023,7 +3072,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":83 + /* "pysam/cvcf.pyx":83 * raise ValueError("Don't understand region string '%s'" % r) * result.append( (chrom,start,end) ) * return result # <<<<<<<<<<<<<< @@ -3044,7 +3093,7 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_12); __Pyx_XDECREF(__pyx_t_13); - __Pyx_AddTraceback("cvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_result); @@ -3060,14 +3109,14 @@ static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_sel } /* Python wrapper */ -static int __pyx_pw_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_vcf = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0}; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0}; PyObject* values[1] = {0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -3080,8 +3129,7 @@ static int __pyx_pw_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; } if (unlikely(kw_args > 0)) { @@ -3098,16 +3146,16 @@ static int __pyx_pw_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_9VCFRecord___init__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self), __pyx_v_vcf); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self), __pyx_v_vcf); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":104 +/* "pysam/cvcf.pyx":104 * cdef uint32_t pos * * def __init__(self, vcf): # <<<<<<<<<<<<<< @@ -3115,12 +3163,12 @@ static int __pyx_pw_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject * # if len(data) != len(self.vcf._samples): */ -static int __pyx_pf_4cvcf_9VCFRecord___init__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf) { +static int __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__", 0); - /* "cvcf.pyx":105 + /* "pysam/cvcf.pyx":105 * * def __init__(self, vcf): * self.vcf = vcf # <<<<<<<<<<<<<< @@ -3139,14 +3187,14 @@ static int __pyx_pf_4cvcf_9VCFRecord___init__(struct __pyx_obj_4cvcf_VCFRecord * } /* Python wrapper */ -static int __pyx_pw_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_vcf = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0}; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0}; PyObject* values[1] = {0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -3159,8 +3207,7 @@ static int __pyx_pw_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; } if (unlikely(kw_args > 0)) { @@ -3177,16 +3224,16 @@ static int __pyx_pw_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCFRecord.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_2__cinit__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self), __pyx_v_vcf); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self), __pyx_v_vcf); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":115 +/* "pysam/cvcf.pyx":115 * # len(data))) * * def __cinit__(self, vcf ): # <<<<<<<<<<<<<< @@ -3194,12 +3241,12 @@ static int __pyx_pw_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject * self.offset = 9 */ -static int __pyx_pf_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf) { +static int __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__", 0); - /* "cvcf.pyx":117 + /* "pysam/cvcf.pyx":117 * def __cinit__(self, vcf ): * # start indexed access at genotypes * self.offset = 9 # <<<<<<<<<<<<<< @@ -3208,7 +3255,7 @@ static int __pyx_pf_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_4cvcf_VCFRecord */ __pyx_v_self->__pyx_base.offset = 9; - /* "cvcf.pyx":119 + /* "pysam/cvcf.pyx":119 * self.offset = 9 * * self.vcf = vcf # <<<<<<<<<<<<<< @@ -3227,20 +3274,20 @@ static int __pyx_pf_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_4cvcf_VCFRecord } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_9VCFRecord_4error[] = "raise error."; -static PyObject *__pyx_pw_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_9VCFRecord_4error[] = "raise error."; +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_line = 0; PyObject *__pyx_v_error = 0; PyObject *__pyx_v_opt = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("error (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0}; PyObject* values[3] = {0,0,0}; - /* "cvcf.pyx":121 + /* "pysam/cvcf.pyx":121 * self.vcf = vcf * * def error(self,line,error,opt=None): # <<<<<<<<<<<<<< @@ -3261,12 +3308,10 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self, PyObje kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -3296,16 +3341,16 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self, PyObje __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCFRecord.error", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.error", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_4error(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self), __pyx_v_line, __pyx_v_error, __pyx_v_opt); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_4error(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self), __pyx_v_line, __pyx_v_error, __pyx_v_opt); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3316,7 +3361,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFReco int __pyx_clineno = 0; __Pyx_RefNannySetupContext("error", 0); - /* "cvcf.pyx":124 + /* "pysam/cvcf.pyx":124 * '''raise error.''' * # pass to vcf file for error handling * return self.vcf.error( line, error, opt ) # <<<<<<<<<<<<<< @@ -3351,7 +3396,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFReco __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("cvcf.VCFRecord.error", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.error", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3359,7 +3404,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFReco return __pyx_r; } -/* "cvcf.pyx":126 +/* "pysam/cvcf.pyx":126 * return self.vcf.error( line, error, opt ) * * cdef update( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<< @@ -3367,7 +3412,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFReco * */ -static PyObject *__pyx_f_4cvcf_9VCFRecord_update(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) { +static PyObject *__pyx_f_5pysam_4cvcf_9VCFRecord_update(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3376,18 +3421,18 @@ static PyObject *__pyx_f_4cvcf_9VCFRecord_update(struct __pyx_obj_4cvcf_VCFRecor int __pyx_clineno = 0; __Pyx_RefNannySetupContext("update", 0); - /* "cvcf.pyx":131 + /* "pysam/cvcf.pyx":131 * nbytes does not include the terminal '\0'. * ''' * TabProxies.TupleProxy.update( self, buffer, nbytes ) # <<<<<<<<<<<<<< * * self.contig = self.fields[0] */ - __pyx_t_1 = __pyx_vtabptr_10TabProxies_TupleProxy->update(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_vtabptr_5pysam_10TabProxies_TupleProxy->update(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":133 + /* "pysam/cvcf.pyx":133 * TabProxies.TupleProxy.update( self, buffer, nbytes ) * * self.contig = self.fields[0] # <<<<<<<<<<<<<< @@ -3396,7 +3441,7 @@ static PyObject *__pyx_f_4cvcf_9VCFRecord_update(struct __pyx_obj_4cvcf_VCFRecor */ __pyx_v_self->contig = (__pyx_v_self->__pyx_base.fields[0]); - /* "cvcf.pyx":135 + /* "pysam/cvcf.pyx":135 * self.contig = self.fields[0] * # vcf counts from 1 - correct here * self.pos = atoi( self.fields[1] ) - 1 # <<<<<<<<<<<<<< @@ -3409,7 +3454,7 @@ static PyObject *__pyx_f_4cvcf_9VCFRecord_update(struct __pyx_obj_4cvcf_VCFRecor goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCFRecord.update", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.update", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3418,17 +3463,17 @@ static PyObject *__pyx_f_4cvcf_9VCFRecord_update(struct __pyx_obj_4cvcf_VCFRecor } /* Python wrapper */ -static Py_ssize_t __pyx_pw_4cvcf_9VCFRecord_7__len__(PyObject *__pyx_v_self); /*proto*/ -static Py_ssize_t __pyx_pw_4cvcf_9VCFRecord_7__len__(PyObject *__pyx_v_self) { +static Py_ssize_t __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__(PyObject *__pyx_v_self); /*proto*/ +static Py_ssize_t __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__(PyObject *__pyx_v_self) { Py_ssize_t __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__len__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_6__len__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_6__len__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":137 +/* "pysam/cvcf.pyx":137 * self.pos = atoi( self.fields[1] ) - 1 * * def __len__(self): # <<<<<<<<<<<<<< @@ -3436,7 +3481,7 @@ static Py_ssize_t __pyx_pw_4cvcf_9VCFRecord_7__len__(PyObject *__pyx_v_self) { * */ -static Py_ssize_t __pyx_pf_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static Py_ssize_t __pyx_pf_5pysam_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { Py_ssize_t __pyx_r; __Pyx_RefNannyDeclarations long __pyx_t_1; @@ -3444,7 +3489,7 @@ static Py_ssize_t __pyx_pf_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_4cvcf_VCFR long __pyx_t_3; __Pyx_RefNannySetupContext("__len__", 0); - /* "cvcf.pyx":138 + /* "pysam/cvcf.pyx":138 * * def __len__(self): * return max(0, self.nfields - 9) # <<<<<<<<<<<<<< @@ -3468,17 +3513,17 @@ static Py_ssize_t __pyx_pf_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_4cvcf_VCFR } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_6contig_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_6contig_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_6contig___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_6contig___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":141 +/* "pysam/cvcf.pyx":141 * * property contig: * def __get__(self): return self.contig # <<<<<<<<<<<<<< @@ -3486,7 +3531,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_6contig_1__get__(PyObject *__pyx_v_se * property pos: */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3505,7 +3550,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_4cvc goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCFRecord.contig.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.contig.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3514,17 +3559,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_4cvc } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_3pos___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_3pos___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":144 +/* "pysam/cvcf.pyx":144 * * property pos: * def __get__(self): return self.pos # <<<<<<<<<<<<<< @@ -3532,7 +3577,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_v_self) * property id: */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3551,7 +3596,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_4cvcf_V goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCFRecord.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3560,17 +3605,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_4cvcf_V } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_2id___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_2id___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":147 +/* "pysam/cvcf.pyx":147 * * property id: * def __get__(self): return self.fields[2] # <<<<<<<<<<<<<< @@ -3578,7 +3623,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v_self) * property ref: */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3597,7 +3642,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_4cvcf_VC goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCFRecord.id.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.id.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3606,17 +3651,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_4cvcf_VC } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_3ref___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":150 +/* "pysam/cvcf.pyx":150 * * property ref: * def __get__(self): return self.fields[3] # <<<<<<<<<<<<<< @@ -3624,7 +3669,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_v_self) * property alt: */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -3643,7 +3688,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_4cvcf_V goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCFRecord.ref.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.ref.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -3652,17 +3697,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_4cvcf_V } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_3alt___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":153 +/* "pysam/cvcf.pyx":153 * * property alt: * def __get__(self): # <<<<<<<<<<<<<< @@ -3670,7 +3715,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_v_self) * alt = self.fields[4] */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_v_alt = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -3682,7 +3727,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_V int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "cvcf.pyx":155 + /* "pysam/cvcf.pyx":155 * def __get__(self): * # convert v3.3 to v4.0 alleles below * alt = self.fields[4] # <<<<<<<<<<<<<< @@ -3694,14 +3739,16 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_V __pyx_v_alt = ((PyObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":156 + /* "pysam/cvcf.pyx":156 * # convert v3.3 to v4.0 alleles below * alt = self.fields[4] * if alt == ".": alt = [] # <<<<<<<<<<<<<< * else: alt = alt.upper().split(',') * return alt */ - __pyx_t_2 = __Pyx_PyString_Equals(__pyx_v_alt, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -3712,7 +3759,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_V } /*else*/ { - /* "cvcf.pyx":157 + /* "pysam/cvcf.pyx":157 * alt = self.fields[4] * if alt == ".": alt = [] * else: alt = alt.upper().split(',') # <<<<<<<<<<<<<< @@ -3736,7 +3783,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_V } __pyx_L3:; - /* "cvcf.pyx":158 + /* "pysam/cvcf.pyx":158 * if alt == ".": alt = [] * else: alt = alt.upper().split(',') * return alt # <<<<<<<<<<<<<< @@ -3753,7 +3800,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_V __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("cvcf.VCFRecord.alt.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.alt.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_alt); @@ -3763,17 +3810,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_V } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_4qual___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":161 +/* "pysam/cvcf.pyx":161 * * property qual: * def __get__(self): # <<<<<<<<<<<<<< @@ -3781,7 +3828,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx_v_self * if qual == b".": qual = -1 */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_v_qual = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -3802,7 +3849,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "cvcf.pyx":162 + /* "pysam/cvcf.pyx":162 * property qual: * def __get__(self): * qual = self.fields[5] # <<<<<<<<<<<<<< @@ -3814,14 +3861,16 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_ __pyx_v_qual = ((PyObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":163 + /* "pysam/cvcf.pyx":163 * def __get__(self): * qual = self.fields[5] * if qual == b".": qual = -1 # <<<<<<<<<<<<<< * else: * try: qual = float(qual) */ - __pyx_t_2 = __Pyx_PyBytes_Equals(__pyx_v_qual, ((PyObject *)__pyx_kp_b_9), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, ((PyObject *)__pyx_kp_b_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { __Pyx_INCREF(__pyx_int_neg_1); __Pyx_DECREF(__pyx_v_qual); @@ -3830,7 +3879,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_ } /*else*/ { - /* "cvcf.pyx":165 + /* "pysam/cvcf.pyx":165 * if qual == b".": qual = -1 * else: * try: qual = float(qual) # <<<<<<<<<<<<<< @@ -3857,7 +3906,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_ __pyx_L4_error:; __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":166 + /* "pysam/cvcf.pyx":166 * else: * try: qual = float(qual) * except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL) # <<<<<<<<<<<<<< @@ -3865,7 +3914,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_ * property filter: */ /*except:*/ { - __Pyx_AddTraceback("cvcf.VCFRecord.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_7, &__pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_GOTREF(__pyx_t_7); @@ -3926,7 +3975,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_ __Pyx_XDECREF(__pyx_t_10); __Pyx_XDECREF(__pyx_t_11); __Pyx_XDECREF(__pyx_t_12); - __Pyx_AddTraceback("cvcf.VCFRecord.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_qual); @@ -3936,17 +3985,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_6filter_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_6filter_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_6filter___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":169 +/* "pysam/cvcf.pyx":169 * * property filter: * def __get__(self): # <<<<<<<<<<<<<< @@ -3954,7 +4003,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_6filter_1__get__(PyObject *__pyx_v_se * # postpone checking that filters exist. Encode missing filter or no filtering as empty list */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { char *__pyx_v_f; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -3969,7 +4018,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvc int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "cvcf.pyx":170 + /* "pysam/cvcf.pyx":170 * property filter: * def __get__(self): * f = self.fields[6] # <<<<<<<<<<<<<< @@ -3978,7 +4027,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvc */ __pyx_v_f = (__pyx_v_self->__pyx_base.fields[6]); - /* "cvcf.pyx":172 + /* "pysam/cvcf.pyx":172 * f = self.fields[6] * # postpone checking that filters exist. Encode missing filter or no filtering as empty list * if f == b"." or f == b"PASS" or f == b"0": return [] # <<<<<<<<<<<<<< @@ -3987,24 +4036,21 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvc */ __pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (!__pyx_t_3) { __pyx_t_2 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); - __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_n_b__PASS), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_n_b__PASS), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (!__pyx_t_4) { __pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b__0), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b__0), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -4027,7 +4073,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvc } /*else*/ { - /* "cvcf.pyx":173 + /* "pysam/cvcf.pyx":173 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list * if f == b"." or f == b"PASS" or f == b"0": return [] * else: return f.split(';') # <<<<<<<<<<<<<< @@ -4054,7 +4100,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvc __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("cvcf.VCFRecord.filter.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.filter.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -4063,17 +4109,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvc } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_4info_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_4info_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_4info___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":176 +/* "pysam/cvcf.pyx":176 * * property info: * def __get__(self): # <<<<<<<<<<<<<< @@ -4081,7 +4127,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_4info_1__get__(PyObject *__pyx_v_self * # dictionary of keys, and list of values */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { char *__pyx_v_col; PyObject *__pyx_v_info = NULL; PyObject *__pyx_v_blurp = NULL; @@ -4104,7 +4150,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "cvcf.pyx":177 + /* "pysam/cvcf.pyx":177 * property info: * def __get__(self): * col = self.fields[7] # <<<<<<<<<<<<<< @@ -4113,7 +4159,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ */ __pyx_v_col = (__pyx_v_self->__pyx_base.fields[7]); - /* "cvcf.pyx":179 + /* "pysam/cvcf.pyx":179 * col = self.fields[7] * # dictionary of keys, and list of values * info = {} # <<<<<<<<<<<<<< @@ -4125,7 +4171,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ __pyx_v_info = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":180 + /* "pysam/cvcf.pyx":180 * # dictionary of keys, and list of values * info = {} * if col != b".": # <<<<<<<<<<<<<< @@ -4134,14 +4180,13 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ */ __pyx_t_1 = PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":181 + /* "pysam/cvcf.pyx":181 * info = {} * if col != b".": * for blurp in col.split(';'): # <<<<<<<<<<<<<< @@ -4168,10 +4213,18 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ for (;;) { if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_2 = __pyx_t_5(__pyx_t_1); if (unlikely(!__pyx_t_2)) { @@ -4187,7 +4240,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ __pyx_v_blurp = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":182 + /* "pysam/cvcf.pyx":182 * if col != b".": * for blurp in col.split(';'): * elts = blurp.split('=') # <<<<<<<<<<<<<< @@ -4203,7 +4256,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ __pyx_v_elts = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":183 + /* "pysam/cvcf.pyx":183 * for blurp in col.split(';'): * elts = blurp.split('=') * if len(elts) == 1: v = None # <<<<<<<<<<<<<< @@ -4219,7 +4272,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ goto __pyx_L6; } - /* "cvcf.pyx":184 + /* "pysam/cvcf.pyx":184 * elts = blurp.split('=') * if len(elts) == 1: v = None * elif len(elts) == 2: v = elts[1] # <<<<<<<<<<<<<< @@ -4238,7 +4291,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ } /*else*/ { - /* "cvcf.pyx":185 + /* "pysam/cvcf.pyx":185 * if len(elts) == 1: v = None * elif len(elts) == 2: v = elts[1] * else: self.vcf.error(str(self),self.ERROR_INFO_STRING) # <<<<<<<<<<<<<< @@ -4273,7 +4326,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ } __pyx_L6:; - /* "cvcf.pyx":186 + /* "pysam/cvcf.pyx":186 * elif len(elts) == 2: v = elts[1] * else: self.vcf.error(str(self),self.ERROR_INFO_STRING) * info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self)) # <<<<<<<<<<<<<< @@ -4324,7 +4377,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ } __pyx_L3:; - /* "cvcf.pyx":187 + /* "pysam/cvcf.pyx":187 * else: self.vcf.error(str(self),self.ERROR_INFO_STRING) * info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self)) * return info # <<<<<<<<<<<<<< @@ -4345,7 +4398,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ __Pyx_XDECREF(__pyx_t_8); __Pyx_XDECREF(__pyx_t_9); __Pyx_XDECREF(__pyx_t_10); - __Pyx_AddTraceback("cvcf.VCFRecord.info.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.info.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_info); @@ -4358,17 +4411,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_6format_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_6format_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_6format___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":190 +/* "pysam/cvcf.pyx":190 * * property format: * def __get__(self): # <<<<<<<<<<<<<< @@ -4376,7 +4429,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_6format_1__get__(PyObject *__pyx_v_se * */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -4386,7 +4439,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_4cvc int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "cvcf.pyx":191 + /* "pysam/cvcf.pyx":191 * property format: * def __get__(self): * return self.fields[8].split(':') # <<<<<<<<<<<<<< @@ -4411,7 +4464,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_4cvc __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("cvcf.VCFRecord.format.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.format.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -4420,17 +4473,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_4cvc } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_7samples_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_7samples_1__get__(PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_7samples___get__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":194 +/* "pysam/cvcf.pyx":194 * * property samples: * def __get__(self): # <<<<<<<<<<<<<< @@ -4438,7 +4491,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_7samples_1__get__(PyObject *__pyx_v_s * */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -4447,7 +4500,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_4cv int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__get__", 0); - /* "cvcf.pyx":195 + /* "pysam/cvcf.pyx":195 * property samples: * def __get__(self): * return self.vcf._samples # <<<<<<<<<<<<<< @@ -4465,7 +4518,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_4cv goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCFRecord.samples.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.samples.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -4474,17 +4527,17 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_4cv } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/ -static PyObject *__pyx_pw_4cvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) { +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0); - __pyx_r = __pyx_pf_4cvcf_9VCFRecord_8__getitem__(((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_v_self), ((PyObject *)__pyx_v_key)); + __pyx_r = __pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_v_self), ((PyObject *)__pyx_v_key)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":197 +/* "pysam/cvcf.pyx":197 * return self.vcf._samples * * def __getitem__(self, key): # <<<<<<<<<<<<<< @@ -4492,7 +4545,7 @@ static PyObject *__pyx_pw_4cvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v_self, * # parse sample columns */ -static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key) { +static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key) { PyObject *__pyx_v_values = NULL; PyObject *__pyx_v_alt = NULL; PyObject *__pyx_v_format = NULL; @@ -4520,7 +4573,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__getitem__", 0); - /* "cvcf.pyx":200 + /* "pysam/cvcf.pyx":200 * * # parse sample columns * values = self.fields[self.vcf._sample2column[key]].split(':') # <<<<<<<<<<<<<< @@ -4545,7 +4598,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_v_values = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":201 + /* "pysam/cvcf.pyx":201 * # parse sample columns * values = self.fields[self.vcf._sample2column[key]].split(':') * alt = self.alt # <<<<<<<<<<<<<< @@ -4557,7 +4610,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_v_alt = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":202 + /* "pysam/cvcf.pyx":202 * values = self.fields[self.vcf._sample2column[key]].split(':') * alt = self.alt * format = self.format # <<<<<<<<<<<<<< @@ -4569,7 +4622,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_v_format = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":204 + /* "pysam/cvcf.pyx":204 * format = self.format * * if len(values) > len(format): # <<<<<<<<<<<<<< @@ -4581,7 +4634,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_t_5 = (__pyx_t_3 > __pyx_t_4); if (__pyx_t_5) { - /* "cvcf.pyx":205 + /* "pysam/cvcf.pyx":205 * * if len(values) > len(format): * self.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ # <<<<<<<<<<<<<< @@ -4603,7 +4656,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_18); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - /* "cvcf.pyx":206 + /* "pysam/cvcf.pyx":206 * if len(values) > len(format): * self.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ * (len(values),key,len(format))) # <<<<<<<<<<<<<< @@ -4650,7 +4703,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } __pyx_L3:; - /* "cvcf.pyx":208 + /* "pysam/cvcf.pyx":208 * (len(values),key,len(format))) * * result = {} # <<<<<<<<<<<<<< @@ -4662,7 +4715,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_v_result = __pyx_t_8; __pyx_t_8 = 0; - /* "cvcf.pyx":209 + /* "pysam/cvcf.pyx":209 * * result = {} * for idx in range(len(format)): # <<<<<<<<<<<<<< @@ -4692,10 +4745,18 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V for (;;) { if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break; - __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break; - __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_8 = __pyx_t_10(__pyx_t_9); if (unlikely(!__pyx_t_8)) { @@ -4711,7 +4772,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_v_idx = __pyx_t_8; __pyx_t_8 = 0; - /* "cvcf.pyx":210 + /* "pysam/cvcf.pyx":210 * result = {} * for idx in range(len(format)): * expected = self.vcf.get_expected(format[idx], self.vcf._format, alt) # <<<<<<<<<<<<<< @@ -4743,7 +4804,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_v_expected = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":211 + /* "pysam/cvcf.pyx":211 * for idx in range(len(format)): * expected = self.vcf.get_expected(format[idx], self.vcf._format, alt) * if idx < len(values): value = values[idx] # <<<<<<<<<<<<<< @@ -4753,8 +4814,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - __pyx_t_1 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -4768,15 +4828,14 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } /*else*/ { - /* "cvcf.pyx":213 + /* "pysam/cvcf.pyx":213 * if idx < len(values): value = values[idx] * else: * if expected == -1: value = "." # <<<<<<<<<<<<<< * else: value = ",".join(["."]*expected) * */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_5) { @@ -4787,7 +4846,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } /*else*/ { - /* "cvcf.pyx":214 + /* "pysam/cvcf.pyx":214 * else: * if expected == -1: value = "." * else: value = ",".join(["."]*expected) # <<<<<<<<<<<<<< @@ -4823,7 +4882,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } __pyx_L6:; - /* "cvcf.pyx":216 + /* "pysam/cvcf.pyx":216 * else: value = ",".join(["."]*expected) * * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data)) # <<<<<<<<<<<<<< @@ -4870,15 +4929,14 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":217 + /* "pysam/cvcf.pyx":217 * * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data)) * if expected != -1 and len(result[format[idx]]) != expected: # <<<<<<<<<<<<<< * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) */ - __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_5) { @@ -4891,8 +4949,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -4902,7 +4959,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } if (__pyx_t_12) { - /* "cvcf.pyx":218 + /* "pysam/cvcf.pyx":218 * result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data)) * if expected != -1 and len(result[format[idx]]) != expected: * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, # <<<<<<<<<<<<<< @@ -4924,7 +4981,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_20); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - /* "cvcf.pyx":219 + /* "pysam/cvcf.pyx":219 * if expected != -1 and len(result[format[idx]]) != expected: * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) # <<<<<<<<<<<<<< @@ -4969,7 +5026,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; - /* "cvcf.pyx":220 + /* "pysam/cvcf.pyx":220 * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) * if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]])) # <<<<<<<<<<<<<< @@ -4985,8 +5042,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_13 = PyObject_RichCompare(__pyx_t_8, __pyx_v_expected, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_13); + __pyx_t_13 = PyObject_RichCompare(__pyx_t_8, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_13); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; @@ -5037,7 +5093,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } __pyx_L9:; - /* "cvcf.pyx":221 + /* "pysam/cvcf.pyx":221 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) * if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]])) * result[format[idx]] = result[format[idx]][:expected] # <<<<<<<<<<<<<< @@ -5064,7 +5120,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "cvcf.pyx":223 + /* "pysam/cvcf.pyx":223 * result[format[idx]] = result[format[idx]][:expected] * * return result # <<<<<<<<<<<<<< @@ -5086,7 +5142,7 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V __Pyx_XDECREF(__pyx_t_8); __Pyx_XDECREF(__pyx_t_9); __Pyx_XDECREF(__pyx_t_13); - __Pyx_AddTraceback("cvcf.VCFRecord.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCFRecord.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_values); @@ -5102,14 +5158,14 @@ static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_V } /* Python wrapper */ -static int __pyx_pw_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_vcffile = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcffile,0}; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcffile,0}; PyObject* values[1] = {0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -5122,8 +5178,7 @@ static int __pyx_pw_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObje kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcffile); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcffile)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; } if (unlikely(kw_args > 0)) { @@ -5140,16 +5195,16 @@ static int __pyx_pw_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObje __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.asVCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.asVCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_11asVCFRecord___init__(((struct __pyx_obj_4cvcf_asVCFRecord *)__pyx_v_self), __pyx_v_vcffile); + __pyx_r = __pyx_pf_5pysam_4cvcf_11asVCFRecord___init__(((struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)__pyx_v_self), __pyx_v_vcffile); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":229 +/* "pysam/cvcf.pyx":229 * '''converts a :term:`tabix row` into a VCF record.''' * cdef vcffile * def __init__(self, vcffile ): # <<<<<<<<<<<<<< @@ -5157,12 +5212,12 @@ static int __pyx_pw_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObje * def __call__(self, char * buffer, int len ): */ -static int __pyx_pf_4cvcf_11asVCFRecord___init__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile) { +static int __pyx_pf_5pysam_4cvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__", 0); - /* "cvcf.pyx":230 + /* "pysam/cvcf.pyx":230 * cdef vcffile * def __init__(self, vcffile ): * self.vcffile = vcffile # <<<<<<<<<<<<<< @@ -5181,15 +5236,15 @@ static int __pyx_pf_4cvcf_11asVCFRecord___init__(struct __pyx_obj_4cvcf_asVCFRec } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyObject *__pyx_pw_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { char *__pyx_v_buffer; int __pyx_v_len; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__call__ (wrapper)", 0); { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -5203,12 +5258,10 @@ static PyObject *__pyx_pw_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -5229,16 +5282,16 @@ static PyObject *__pyx_pw_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.asVCFRecord.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.asVCFRecord.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_11asVCFRecord_2__call__(((struct __pyx_obj_4cvcf_asVCFRecord *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); + __pyx_r = __pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(((struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)__pyx_v_self), __pyx_v_buffer, __pyx_v_len); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":231 +/* "pysam/cvcf.pyx":231 * def __init__(self, vcffile ): * self.vcffile = vcffile * def __call__(self, char * buffer, int len ): # <<<<<<<<<<<<<< @@ -5246,8 +5299,8 @@ static PyObject *__pyx_pw_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, * r = VCFRecord( self.vcffile ) */ -static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { - struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_r = 0; +static PyObject *__pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len) { + struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_r = 0; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -5257,7 +5310,7 @@ static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_a int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__call__", 0); - /* "cvcf.pyx":233 + /* "pysam/cvcf.pyx":233 * def __call__(self, char * buffer, int len ): * cdef VCFRecord r * r = VCFRecord( self.vcffile ) # <<<<<<<<<<<<<< @@ -5269,24 +5322,24 @@ static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_a __Pyx_INCREF(__pyx_v_self->vcffile); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->vcffile); __Pyx_GIVEREF(__pyx_v_self->vcffile); - __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_4cvcf_VCFRecord)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_4cvcf_VCFRecord)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_v_r = ((struct __pyx_obj_4cvcf_VCFRecord *)__pyx_t_2); + __pyx_v_r = ((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":234 + /* "pysam/cvcf.pyx":234 * cdef VCFRecord r * r = VCFRecord( self.vcffile ) * r.copy( buffer, len ) # <<<<<<<<<<<<<< * return r * */ - __pyx_t_2 = ((struct __pyx_vtabstruct_4cvcf_VCFRecord *)__pyx_v_r->__pyx_base.__pyx_vtab)->__pyx_base.copy(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *)__pyx_v_r->__pyx_base.__pyx_vtab)->__pyx_base.copy(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":235 + /* "pysam/cvcf.pyx":235 * r = VCFRecord( self.vcffile ) * r.copy( buffer, len ) * return r # <<<<<<<<<<<<<< @@ -5303,7 +5356,7 @@ static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_a __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); - __Pyx_AddTraceback("cvcf.asVCFRecord.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.asVCFRecord.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_r); @@ -5312,7 +5365,7 @@ static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_a return __pyx_r; } -/* "cvcf.pyx":314 +/* "pysam/cvcf.pyx":314 * _lines = None * * def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # <<<<<<<<<<<<<< @@ -5320,7 +5373,7 @@ static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_a * for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id */ -static PyObject *__pyx_pf_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -5354,7 +5407,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__py goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -5363,21 +5416,20 @@ static PyObject *__pyx_pf_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_4cvcf_3VCF_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v__copy = 0; PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_regions = 0; PyObject *__pyx_v_lines = 0; PyObject *__pyx_v_leftalign = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s___copy,&__pyx_n_s__reference,&__pyx_n_s__regions,&__pyx_n_s__lines,&__pyx_n_s__leftalign,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s___copy,&__pyx_n_s__reference,&__pyx_n_s__regions,&__pyx_n_s__lines,&__pyx_n_s__leftalign,0}; PyObject* values[6] = {0,0,0,0,0,0}; __pyx_defaults *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults, __pyx_self); values[1] = ((PyObject *)((PyObject *)Py_None)); @@ -5401,8 +5453,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyObject *_ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (kw_args > 0) { @@ -5456,16 +5507,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyObject *_ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF___init__(__pyx_self, __pyx_v_self, __pyx_v__copy, __pyx_v_reference, __pyx_v_regions, __pyx_v_lines, __pyx_v_leftalign); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF___init__(__pyx_self, __pyx_v_self, __pyx_v__copy, __pyx_v_reference, __pyx_v_regions, __pyx_v_lines, __pyx_v_leftalign); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign) { PyObject *__pyx_v_id = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -5481,7 +5532,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); - /* "cvcf.pyx":316 + /* "pysam/cvcf.pyx":316 * def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): * # make error identifiers accessible by name * for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id # <<<<<<<<<<<<<< @@ -5508,10 +5559,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self for (;;) { if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; - __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_1 = __pyx_t_4(__pyx_t_2); if (unlikely(!__pyx_t_1)) { @@ -5548,20 +5607,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":317 + /* "pysam/cvcf.pyx":317 * # make error identifiers accessible by name * for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id * if _copy != None: # <<<<<<<<<<<<<< * self._leftalign = _copy._leftalign * self._header = _copy._header[:] */ - __pyx_t_2 = PyObject_RichCompare(__pyx_v__copy, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v__copy, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_7) { - /* "cvcf.pyx":318 + /* "pysam/cvcf.pyx":318 * for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id * if _copy != None: * self._leftalign = _copy._leftalign # <<<<<<<<<<<<<< @@ -5573,7 +5631,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___leftalign, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":319 + /* "pysam/cvcf.pyx":319 * if _copy != None: * self._leftalign = _copy._leftalign * self._header = _copy._header[:] # <<<<<<<<<<<<<< @@ -5588,7 +5646,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___header, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":320 + /* "pysam/cvcf.pyx":320 * self._leftalign = _copy._leftalign * self._header = _copy._header[:] * self._version = _copy._version # <<<<<<<<<<<<<< @@ -5600,7 +5658,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":321 + /* "pysam/cvcf.pyx":321 * self._header = _copy._header[:] * self._version = _copy._version * self._info = copy.deepcopy(_copy._info) # <<<<<<<<<<<<<< @@ -5626,7 +5684,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___info, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":322 + /* "pysam/cvcf.pyx":322 * self._version = _copy._version * self._info = copy.deepcopy(_copy._info) * self._filter = copy.deepcopy(_copy._filter) # <<<<<<<<<<<<<< @@ -5652,7 +5710,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___filter, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":323 + /* "pysam/cvcf.pyx":323 * self._info = copy.deepcopy(_copy._info) * self._filter = copy.deepcopy(_copy._filter) * self._format = copy.deepcopy(_copy._format) # <<<<<<<<<<<<<< @@ -5678,7 +5736,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___format, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":324 + /* "pysam/cvcf.pyx":324 * self._filter = copy.deepcopy(_copy._filter) * self._format = copy.deepcopy(_copy._format) * self._samples = _copy._samples[:] # <<<<<<<<<<<<<< @@ -5693,7 +5751,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":325 + /* "pysam/cvcf.pyx":325 * self._format = copy.deepcopy(_copy._format) * self._samples = _copy._samples[:] * self._sample2column = copy.deepcopy(_copy._sample2column) # <<<<<<<<<<<<<< @@ -5719,7 +5777,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___sample2column, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":326 + /* "pysam/cvcf.pyx":326 * self._samples = _copy._samples[:] * self._sample2column = copy.deepcopy(_copy._sample2column) * self._ignored_errors = copy.deepcopy(_copy._ignored_errors) # <<<<<<<<<<<<<< @@ -5745,7 +5803,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___ignored_errors, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":327 + /* "pysam/cvcf.pyx":327 * self._sample2column = copy.deepcopy(_copy._sample2column) * self._ignored_errors = copy.deepcopy(_copy._ignored_errors) * self._warn_errors = copy.deepcopy(_copy._warn_errors) # <<<<<<<<<<<<<< @@ -5771,7 +5829,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___warn_errors, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":328 + /* "pysam/cvcf.pyx":328 * self._ignored_errors = copy.deepcopy(_copy._ignored_errors) * self._warn_errors = copy.deepcopy(_copy._warn_errors) * self._reference = _copy._reference # <<<<<<<<<<<<<< @@ -5783,7 +5841,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___reference, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":329 + /* "pysam/cvcf.pyx":329 * self._warn_errors = copy.deepcopy(_copy._warn_errors) * self._reference = _copy._reference * self._regions = _copy._regions # <<<<<<<<<<<<<< @@ -5798,7 +5856,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self } __pyx_L5:; - /* "cvcf.pyx":330 + /* "pysam/cvcf.pyx":330 * self._reference = _copy._reference * self._regions = _copy._regions * if reference: self._reference = reference # <<<<<<<<<<<<<< @@ -5812,7 +5870,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self } __pyx_L6:; - /* "cvcf.pyx":331 + /* "pysam/cvcf.pyx":331 * self._regions = _copy._regions * if reference: self._reference = reference * if regions: self._regions = regions # <<<<<<<<<<<<<< @@ -5826,7 +5884,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self } __pyx_L7:; - /* "cvcf.pyx":332 + /* "pysam/cvcf.pyx":332 * if reference: self._reference = reference * if regions: self._regions = regions * if leftalign: self._leftalign = leftalign # <<<<<<<<<<<<<< @@ -5840,7 +5898,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self } __pyx_L8:; - /* "cvcf.pyx":333 + /* "pysam/cvcf.pyx":333 * if regions: self._regions = regions * if leftalign: self._leftalign = leftalign * self._lines = lines # <<<<<<<<<<<<<< @@ -5856,7 +5914,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("cvcf.VCF.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_id); @@ -5866,22 +5924,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_3error = {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_4cvcf_3VCF_3error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_3error = {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_3error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_line = 0; PyObject *__pyx_v_error = 0; PyObject *__pyx_v_opt = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("error (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0}; PyObject* values[4] = {0,0,0,0}; - /* "cvcf.pyx":335 + /* "pysam/cvcf.pyx":335 * self._lines = lines * * def error(self,line,error,opt=None): # <<<<<<<<<<<<<< @@ -5903,18 +5960,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObject *__py kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -5946,16 +6000,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObject *__py __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.error", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.error", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_2error(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_error, __pyx_v_opt); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_2error(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_error, __pyx_v_opt); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt) { PyObject *__pyx_v_errorlabel = NULL; PyObject *__pyx_v_errorstring = NULL; PyObject *__pyx_v_errwarn = NULL; @@ -5972,7 +6026,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_clineno = 0; __Pyx_RefNannySetupContext("error", 0); - /* "cvcf.pyx":336 + /* "pysam/cvcf.pyx":336 * * def error(self,line,error,opt=None): * if error in self._ignored_errors: return # <<<<<<<<<<<<<< @@ -5981,7 +6035,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = ((PySequence_Contains(__pyx_t_1, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_1, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { __Pyx_XDECREF(__pyx_r); @@ -5991,7 +6045,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_L3:; - /* "cvcf.pyx":337 + /* "pysam/cvcf.pyx":337 * def error(self,line,error,opt=None): * if error in self._ignored_errors: return * errorlabel, errorstring = self._errors[error].split(':') # <<<<<<<<<<<<<< @@ -6011,27 +6065,33 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) { PyObject* sequence = __pyx_t_3; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) { - if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_4 = PyTuple_GET_ITEM(sequence, 1); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 2)) { - if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyList_GET_ITEM(sequence, 0); __pyx_t_4 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_1); __Pyx_INCREF(__pyx_t_4); + #else + __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - } else { + } else + { Py_ssize_t index = -1; __pyx_t_5 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); @@ -6042,12 +6102,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, index = 1; __pyx_t_4 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_4)) goto __pyx_L4_unpacking_failed; __Pyx_GOTREF(__pyx_t_4); if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = NULL; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; goto __pyx_L5_unpacking_done; __pyx_L4_unpacking_failed:; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_6 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L5_unpacking_done:; } @@ -6056,7 +6117,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, __pyx_v_errorstring = __pyx_t_4; __pyx_t_4 = 0; - /* "cvcf.pyx":338 + /* "pysam/cvcf.pyx":338 * if error in self._ignored_errors: return * errorlabel, errorstring = self._errors[error].split(':') * if opt: errorstring = errorstring % opt # <<<<<<<<<<<<<< @@ -6074,7 +6135,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_L6:; - /* "cvcf.pyx":339 + /* "pysam/cvcf.pyx":339 * errorlabel, errorstring = self._errors[error].split(':') * if opt: errorstring = errorstring % opt * errwarn = ["Error","Warning"][error in self._warn_errors] # <<<<<<<<<<<<<< @@ -6091,7 +6152,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Warning)); __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_2 = ((PySequence_Contains(__pyx_t_4, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_4, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = __Pyx_GetItemInt_List(((PyObject *)__pyx_t_3), __pyx_t_2, sizeof(int), __Pyx_PyBool_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); @@ -6099,7 +6160,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, __pyx_v_errwarn = __pyx_t_4; __pyx_t_4 = 0; - /* "cvcf.pyx":340 + /* "pysam/cvcf.pyx":340 * if opt: errorstring = errorstring % opt * errwarn = ["Error","Warning"][error in self._warn_errors] * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring) # <<<<<<<<<<<<<< @@ -6135,7 +6196,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, __pyx_v_errorstring = __pyx_t_3; __pyx_t_3 = 0; - /* "cvcf.pyx":341 + /* "pysam/cvcf.pyx":341 * errwarn = ["Error","Warning"][error in self._warn_errors] * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring) * if error in self._warn_errors: return # <<<<<<<<<<<<<< @@ -6144,7 +6205,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, */ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = ((PySequence_Contains(__pyx_t_3, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_3, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_2) { __Pyx_XDECREF(__pyx_r); @@ -6154,7 +6215,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, } __pyx_L7:; - /* "cvcf.pyx":342 + /* "pysam/cvcf.pyx":342 * errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring) * if error in self._warn_errors: return * raise ValueError(errorstring) # <<<<<<<<<<<<<< @@ -6180,7 +6241,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); - __Pyx_AddTraceback("cvcf.VCF.error", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.error", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_errorlabel); @@ -6191,7 +6252,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, return __pyx_r; } -/* "cvcf.pyx":344 +/* "pysam/cvcf.pyx":344 * raise ValueError(errorstring) * * def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<< @@ -6199,7 +6260,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, * if not format.startswith('<'): */ -static PyObject *__pyx_pf_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -6221,7 +6282,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__py goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -6230,19 +6291,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_5parse_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_5parse_format = {__Pyx_NAMESTR("parse_format"), (PyCFunction)__pyx_pw_4cvcf_3VCF_5parse_format, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_5parse_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_5parse_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_5parse_format = {__Pyx_NAMESTR("parse_format"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_5parse_format, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_5parse_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_line = 0; PyObject *__pyx_v_format = 0; PyObject *__pyx_v_filter = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__format,&__pyx_n_s__filter,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("parse_format (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__format,&__pyx_n_s__filter,0}; PyObject* values[4] = {0,0,0,0}; __pyx_defaults1 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults1, __pyx_self); values[3] = __pyx_dynamic_args->__pyx_arg_filter; @@ -6260,18 +6320,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_5parse_format(PyObject *__pyx_self, PyObjec kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -6303,16 +6360,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_5parse_format(PyObject *__pyx_self, PyObjec __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_4parse_format(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_format, __pyx_v_filter); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_4parse_format(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_format, __pyx_v_filter); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter) { PyObject *__pyx_v_data = NULL; PyObject *__pyx_v_idx = NULL; PyObject *__pyx_v_elts = NULL; @@ -6343,7 +6400,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_RefNannySetupContext("parse_format", 0); __Pyx_INCREF(__pyx_v_format); - /* "cvcf.pyx":345 + /* "pysam/cvcf.pyx":345 * * def parse_format(self,line,format,filter=False): * if self._version == 40: # <<<<<<<<<<<<<< @@ -6352,14 +6409,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_40, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_40, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":346 + /* "pysam/cvcf.pyx":346 * def parse_format(self,line,format,filter=False): * if self._version == 40: * if not format.startswith('<'): # <<<<<<<<<<<<<< @@ -6376,7 +6432,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_4 = (!__pyx_t_3); if (__pyx_t_4) { - /* "cvcf.pyx":347 + /* "pysam/cvcf.pyx":347 * if self._version == 40: * if not format.startswith('<'): * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) # <<<<<<<<<<<<<< @@ -6401,7 +6457,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":348 + /* "pysam/cvcf.pyx":348 * if not format.startswith('<'): * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) * format = "<"+format # <<<<<<<<<<<<<< @@ -6417,7 +6473,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L4:; - /* "cvcf.pyx":349 + /* "pysam/cvcf.pyx":349 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) * format = "<"+format * if not format.endswith('>'): # <<<<<<<<<<<<<< @@ -6434,7 +6490,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_3 = (!__pyx_t_4); if (__pyx_t_3) { - /* "cvcf.pyx":350 + /* "pysam/cvcf.pyx":350 * format = "<"+format * if not format.endswith('>'): * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) # <<<<<<<<<<<<<< @@ -6459,7 +6515,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":351 + /* "pysam/cvcf.pyx":351 * if not format.endswith('>'): * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) * format += ">" # <<<<<<<<<<<<<< @@ -6475,7 +6531,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L5:; - /* "cvcf.pyx":352 + /* "pysam/cvcf.pyx":352 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) * format += ">" * format = format[1:-1] # <<<<<<<<<<<<<< @@ -6491,7 +6547,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L3:; - /* "cvcf.pyx":353 + /* "pysam/cvcf.pyx":353 * format += ">" * format = format[1:-1] * data = {'id':None,'number':None,'type':None,'descr':None} # <<<<<<<<<<<<<< @@ -6507,7 +6563,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_v_data = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":354 + /* "pysam/cvcf.pyx":354 * format = format[1:-1] * data = {'id':None,'number':None,'type':None,'descr':None} * idx = 0 # <<<<<<<<<<<<<< @@ -6517,7 +6573,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_INCREF(__pyx_int_0); __pyx_v_idx = __pyx_int_0; - /* "cvcf.pyx":355 + /* "pysam/cvcf.pyx":355 * data = {'id':None,'number':None,'type':None,'descr':None} * idx = 0 * while len(format.strip())>0: # <<<<<<<<<<<<<< @@ -6535,7 +6591,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_3 = (__pyx_t_6 > 0); if (!__pyx_t_3) break; - /* "cvcf.pyx":356 + /* "pysam/cvcf.pyx":356 * idx = 0 * while len(format.strip())>0: * elts = format.strip().split(',') # <<<<<<<<<<<<<< @@ -6557,7 +6613,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_v_elts = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":357 + /* "pysam/cvcf.pyx":357 * while len(format.strip())>0: * elts = format.strip().split(',') * first, rest = elts[0], ','.join(elts[1:]) # <<<<<<<<<<<<<< @@ -6586,7 +6642,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_v_rest = __pyx_t_5; __pyx_t_5 = 0; - /* "cvcf.pyx":358 + /* "pysam/cvcf.pyx":358 * elts = format.strip().split(',') * first, rest = elts[0], ','.join(elts[1:]) * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): # <<<<<<<<<<<<<< @@ -6598,8 +6654,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_31), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -6609,8 +6664,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_33), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; @@ -6625,8 +6679,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_35), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -6641,7 +6694,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } if (__pyx_t_4) { - /* "cvcf.pyx":359 + /* "pysam/cvcf.pyx":359 * first, rest = elts[0], ','.join(elts[1:]) * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) # <<<<<<<<<<<<<< @@ -6650,8 +6703,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -6677,15 +6729,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L9:; - /* "cvcf.pyx":360 + /* "pysam/cvcf.pyx":360 * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<< * first = ["ID=","Number=","Type=","Description="][idx] + first * if first.startswith('ID='): data['id'] = first.split('=')[1] */ - __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_4) { @@ -6710,7 +6761,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L10:; - /* "cvcf.pyx":361 + /* "pysam/cvcf.pyx":361 * if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * first = ["ID=","Number=","Type=","Description="][idx] + first # <<<<<<<<<<<<<< @@ -6744,7 +6795,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L8:; - /* "cvcf.pyx":362 + /* "pysam/cvcf.pyx":362 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * first = ["ID=","Number=","Type=","Description="][idx] + first * if first.startswith('ID='): data['id'] = first.split('=')[1] # <<<<<<<<<<<<<< @@ -6772,7 +6823,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx goto __pyx_L11; } - /* "cvcf.pyx":363 + /* "pysam/cvcf.pyx":363 * first = ["ID=","Number=","Type=","Description="][idx] + first * if first.startswith('ID='): data['id'] = first.split('=')[1] * elif first.startswith('Number='): data['number'] = first.split('=')[1] # <<<<<<<<<<<<<< @@ -6800,7 +6851,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx goto __pyx_L11; } - /* "cvcf.pyx":364 + /* "pysam/cvcf.pyx":364 * if first.startswith('ID='): data['id'] = first.split('=')[1] * elif first.startswith('Number='): data['number'] = first.split('=')[1] * elif first.startswith('Type='): data['type'] = first.split('=')[1] # <<<<<<<<<<<<<< @@ -6828,7 +6879,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx goto __pyx_L11; } - /* "cvcf.pyx":365 + /* "pysam/cvcf.pyx":365 * elif first.startswith('Number='): data['number'] = first.split('=')[1] * elif first.startswith('Type='): data['type'] = first.split('=')[1] * elif first.startswith('Description='): # <<<<<<<<<<<<<< @@ -6844,7 +6895,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_4) { - /* "cvcf.pyx":366 + /* "pysam/cvcf.pyx":366 * elif first.startswith('Type='): data['type'] = first.split('=')[1] * elif first.startswith('Description='): * elts = format.split('"') # <<<<<<<<<<<<<< @@ -6860,7 +6911,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_v_elts = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":367 + /* "pysam/cvcf.pyx":367 * elif first.startswith('Description='): * elts = format.split('"') * if len(elts)<3: # <<<<<<<<<<<<<< @@ -6871,7 +6922,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_4 = (__pyx_t_6 < 3); if (__pyx_t_4) { - /* "cvcf.pyx":368 + /* "pysam/cvcf.pyx":368 * elts = format.split('"') * if len(elts)<3: * self.error(line,self.FORMAT_MISSING_QUOTES) # <<<<<<<<<<<<<< @@ -6896,7 +6947,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":369 + /* "pysam/cvcf.pyx":369 * if len(elts)<3: * self.error(line,self.FORMAT_MISSING_QUOTES) * elts = first.split('=') + [rest] # <<<<<<<<<<<<<< @@ -6924,7 +6975,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L12:; - /* "cvcf.pyx":370 + /* "pysam/cvcf.pyx":370 * self.error(line,self.FORMAT_MISSING_QUOTES) * elts = first.split('=') + [rest] * data['descr'] = elts[1] # <<<<<<<<<<<<<< @@ -6936,7 +6987,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - /* "cvcf.pyx":371 + /* "pysam/cvcf.pyx":371 * elts = first.split('=') + [rest] * data['descr'] = elts[1] * rest = '"'.join(elts[2:]) # <<<<<<<<<<<<<< @@ -6960,7 +7011,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_v_rest = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":372 + /* "pysam/cvcf.pyx":372 * data['descr'] = elts[1] * rest = '"'.join(elts[2:]) * if rest.startswith(','): rest = rest[1:] # <<<<<<<<<<<<<< @@ -6987,7 +7038,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } /*else*/ { - /* "cvcf.pyx":374 + /* "pysam/cvcf.pyx":374 * if rest.startswith(','): rest = rest[1:] * else: * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<< @@ -7014,7 +7065,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L11:; - /* "cvcf.pyx":375 + /* "pysam/cvcf.pyx":375 * else: * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * format = rest # <<<<<<<<<<<<<< @@ -7025,7 +7076,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_DECREF(__pyx_v_format); __pyx_v_format = __pyx_v_rest; - /* "cvcf.pyx":376 + /* "pysam/cvcf.pyx":376 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * format = rest * idx += 1 # <<<<<<<<<<<<<< @@ -7038,7 +7089,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_v_idx = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":377 + /* "pysam/cvcf.pyx":377 * format = rest * idx += 1 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings # <<<<<<<<<<<<<< @@ -7047,8 +7098,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { - __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_9 = __pyx_t_3; @@ -7064,7 +7114,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_L14:; } - /* "cvcf.pyx":378 + /* "pysam/cvcf.pyx":378 * idx += 1 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings * if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<< @@ -7098,17 +7148,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L15:; - /* "cvcf.pyx":379 + /* "pysam/cvcf.pyx":379 * if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings * if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * if 'descr' not in data: # <<<<<<<<<<<<<< * # missing description * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) */ - __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = (__Pyx_PyDict_Contains(((PyObject *)__pyx_n_s__descr), ((PyObject *)__pyx_v_data), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { - /* "cvcf.pyx":381 + /* "pysam/cvcf.pyx":381 * if 'descr' not in data: * # missing description * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<< @@ -7133,7 +7183,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":382 + /* "pysam/cvcf.pyx":382 * # missing description * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * data['descr'] = "" # <<<<<<<<<<<<<< @@ -7145,7 +7195,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L16:; - /* "cvcf.pyx":383 + /* "pysam/cvcf.pyx":383 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * data['descr'] = "" * if not data['type'] and not data['number']: # <<<<<<<<<<<<<< @@ -7169,7 +7219,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } if (__pyx_t_4) { - /* "cvcf.pyx":385 + /* "pysam/cvcf.pyx":385 * if not data['type'] and not data['number']: * # fine, ##filter format * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') # <<<<<<<<<<<<<< @@ -7216,7 +7266,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L17:; - /* "cvcf.pyx":386 + /* "pysam/cvcf.pyx":386 * # fine, ##filter format * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') * if not data['type'] in ["Integer","Float","Character","String","Flag"]: # <<<<<<<<<<<<<< @@ -7225,27 +7275,37 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (!((int)__pyx_t_4)) { - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_3 = ((int)__pyx_t_9); } else { __pyx_t_3 = ((int)__pyx_t_4); } if (!__pyx_t_3) { - __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Character), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Character), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_9 = ((int)__pyx_t_4); } else { __pyx_t_9 = __pyx_t_3; } if (!__pyx_t_9) { - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__String), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__String), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_4 = ((int)__pyx_t_3); } else { __pyx_t_4 = __pyx_t_9; } if (!__pyx_t_4) { - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_3 = ((int)__pyx_t_9); } else { __pyx_t_3 = __pyx_t_4; @@ -7254,7 +7314,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_t_4 = (!__pyx_t_3); if (__pyx_t_4) { - /* "cvcf.pyx":387 + /* "pysam/cvcf.pyx":387 * return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') * if not data['type'] in ["Integer","Float","Character","String","Flag"]: * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<< @@ -7282,7 +7342,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L18:; - /* "cvcf.pyx":389 + /* "pysam/cvcf.pyx":389 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * # I would like a missing-value field, but it isn't there * if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value # <<<<<<<<<<<<<< @@ -7291,9 +7351,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (!((int)__pyx_t_4)) { - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_9 = ((int)__pyx_t_3); } else { __pyx_t_9 = ((int)__pyx_t_4); @@ -7306,7 +7370,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } /*else*/ { - /* "cvcf.pyx":390 + /* "pysam/cvcf.pyx":390 * # I would like a missing-value field, but it isn't there * if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value * else: data['missing'] = '.' # <<<<<<<<<<<<<< @@ -7317,7 +7381,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L19:; - /* "cvcf.pyx":391 + /* "pysam/cvcf.pyx":391 * if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value * else: data['missing'] = '.' * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<< @@ -7351,7 +7415,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L20:; - /* "cvcf.pyx":392 + /* "pysam/cvcf.pyx":392 * else: data['missing'] = '.' * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * try: # <<<<<<<<<<<<<< @@ -7365,7 +7429,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_XGOTREF(__pyx_t_13); /*try:*/ { - /* "cvcf.pyx":393 + /* "pysam/cvcf.pyx":393 * if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * try: * n = int(data['number']) # <<<<<<<<<<<<<< @@ -7385,7 +7449,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_v_n = __pyx_t_5; __pyx_t_5 = 0; - /* "cvcf.pyx":394 + /* "pysam/cvcf.pyx":394 * try: * n = int(data['number']) * t = self.NT_NUMBER # <<<<<<<<<<<<<< @@ -7408,7 +7472,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":395 + /* "pysam/cvcf.pyx":395 * n = int(data['number']) * t = self.NT_NUMBER * except ValueError: # <<<<<<<<<<<<<< @@ -7417,13 +7481,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_14 = PyErr_ExceptionMatches(__pyx_builtin_ValueError); if (__pyx_t_14) { - __Pyx_AddTraceback("cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_1, &__pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_GOTREF(__pyx_t_1); __Pyx_GOTREF(__pyx_t_10); - /* "cvcf.pyx":396 + /* "pysam/cvcf.pyx":396 * t = self.NT_NUMBER * except ValueError: * n = -1 # <<<<<<<<<<<<<< @@ -7434,7 +7498,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_XDECREF(__pyx_v_n); __pyx_v_n = __pyx_int_neg_1; - /* "cvcf.pyx":397 + /* "pysam/cvcf.pyx":397 * except ValueError: * n = -1 * if data['number'] == '.': t = self.NT_UNKNOWN # <<<<<<<<<<<<<< @@ -7443,27 +7507,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_9) { - __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_XDECREF(__pyx_v_t); - __pyx_v_t = __pyx_t_7; - __pyx_t_7 = 0; + __pyx_v_t = __pyx_t_2; + __pyx_t_2 = 0; goto __pyx_L31; } - /* "cvcf.pyx":398 + /* "pysam/cvcf.pyx":398 * n = -1 * if data['number'] == '.': t = self.NT_UNKNOWN * elif data['number'] == '#alleles': t = self.NT_ALLELES # <<<<<<<<<<<<<< * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES */ - __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_53), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_53), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (__pyx_t_9) { __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} @@ -7474,7 +7542,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx goto __pyx_L31; } - /* "cvcf.pyx":399 + /* "pysam/cvcf.pyx":399 * if data['number'] == '.': t = self.NT_UNKNOWN * elif data['number'] == '#alleles': t = self.NT_ALLELES * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES # <<<<<<<<<<<<<< @@ -7483,27 +7551,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_54), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_54), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_9) { - __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_XDECREF(__pyx_v_t); - __pyx_v_t = __pyx_t_7; - __pyx_t_7 = 0; + __pyx_v_t = __pyx_t_2; + __pyx_t_2 = 0; goto __pyx_L31; } - /* "cvcf.pyx":400 + /* "pysam/cvcf.pyx":400 * elif data['number'] == '#alleles': t = self.NT_ALLELES * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES # <<<<<<<<<<<<<< * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES */ - __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_55), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_55), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (__pyx_t_9) { __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} @@ -7514,7 +7586,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx goto __pyx_L31; } - /* "cvcf.pyx":401 + /* "pysam/cvcf.pyx":401 * elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # <<<<<<<<<<<<<< @@ -7523,27 +7595,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_9) { - __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_XDECREF(__pyx_v_t); - __pyx_v_t = __pyx_t_7; - __pyx_t_7 = 0; + __pyx_v_t = __pyx_t_2; + __pyx_t_2 = 0; goto __pyx_L31; } - /* "cvcf.pyx":402 + /* "pysam/cvcf.pyx":402 * elif data['number'] == '#genotypes': t = self.NT_GENOTYPES * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # <<<<<<<<<<<<<< * # abbreviations added in VCF version v4.1 * elif data['number'] == 'A': t = self.NT_ALLELES */ - __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_56), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (__pyx_t_9) { __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} @@ -7554,7 +7630,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx goto __pyx_L31; } - /* "cvcf.pyx":404 + /* "pysam/cvcf.pyx":404 * elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES * # abbreviations added in VCF version v4.1 * elif data['number'] == 'A': t = self.NT_ALLELES # <<<<<<<<<<<<<< @@ -7563,27 +7639,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_n_s__A), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_n_s__A), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_9) { - __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_XDECREF(__pyx_v_t); - __pyx_v_t = __pyx_t_7; - __pyx_t_7 = 0; + __pyx_v_t = __pyx_t_2; + __pyx_t_2 = 0; goto __pyx_L31; } - /* "cvcf.pyx":405 + /* "pysam/cvcf.pyx":405 * # abbreviations added in VCF version v4.1 * elif data['number'] == 'A': t = self.NT_ALLELES * elif data['number'] == 'G': t = self.NT_GENOTYPES # <<<<<<<<<<<<<< * else: * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) */ - __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} - __Pyx_GOTREF(__pyx_t_7); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_n_s__G), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__G), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (__pyx_t_9) { __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;} @@ -7595,7 +7675,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } /*else*/ { - /* "cvcf.pyx":407 + /* "pysam/cvcf.pyx":407 * elif data['number'] == 'G': t = self.NT_GENOTYPES * else: * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<< @@ -7640,54 +7720,55 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __pyx_L28_try_end:; } - /* "cvcf.pyx":409 + /* "pysam/cvcf.pyx":409 * self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * # if number is 0 - type must be Flag * if n == 0 and data['type'] != 'Flag': # <<<<<<<<<<<<<< * self.error( line, self.ZERO_FOR_NON_FLAG_FIELD) * # force type 'Flag' if no number */ - __pyx_t_10 = PyObject_RichCompare(__pyx_v_n, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_10 = PyObject_RichCompare(__pyx_v_n, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_9) { __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Flag), Py_NE); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Flag), Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_3 = __pyx_t_4; } else { __pyx_t_3 = __pyx_t_9; } if (__pyx_t_3) { - /* "cvcf.pyx":410 + /* "pysam/cvcf.pyx":410 * # if number is 0 - type must be Flag * if n == 0 and data['type'] != 'Flag': * self.error( line, self.ZERO_FOR_NON_FLAG_FIELD) # <<<<<<<<<<<<<< * # force type 'Flag' if no number * data['type'] = 'Flag' */ - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_57); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_57); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_INCREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1); - __Pyx_GIVEREF(__pyx_t_1); - __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; + PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_10); + __Pyx_GIVEREF(__pyx_t_10); + __pyx_t_10 = 0; + __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - /* "cvcf.pyx":412 + /* "pysam/cvcf.pyx":412 * self.error( line, self.ZERO_FOR_NON_FLAG_FIELD) * # force type 'Flag' if no number * data['type'] = 'Flag' # <<<<<<<<<<<<<< @@ -7699,7 +7780,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx } __pyx_L32:; - /* "cvcf.pyx":414 + /* "pysam/cvcf.pyx":414 * data['type'] = 'Flag' * * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) # <<<<<<<<<<<<<< @@ -7707,13 +7788,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx * def format_format( self, fmt, filter=False ): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); if (unlikely(!__pyx_v_t)) { __Pyx_RaiseUnboundLocalError("t"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_15 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing)); if (!__pyx_t_15) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -7728,19 +7809,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_INCREF(__pyx_v_n); PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_v_n); __Pyx_GIVEREF(__pyx_v_n); - PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_10); - __Pyx_GIVEREF(__pyx_t_10); + PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_1); + __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_t_15); __Pyx_GIVEREF(__pyx_t_15); __pyx_t_5 = 0; - __pyx_t_10 = 0; + __pyx_t_1 = 0; __pyx_t_2 = 0; __pyx_t_15 = 0; - __pyx_t_15 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_15 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_15); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_r = __pyx_t_15; __pyx_t_15 = 0; @@ -7755,7 +7836,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx __Pyx_XDECREF(__pyx_t_7); __Pyx_XDECREF(__pyx_t_10); __Pyx_XDECREF(__pyx_t_15); - __Pyx_AddTraceback("cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_data); @@ -7771,7 +7852,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx return __pyx_r; } -/* "cvcf.pyx":416 +/* "pysam/cvcf.pyx":416 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) * * def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<< @@ -7779,7 +7860,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx * if fmt.number != None and not filter: */ -static PyObject *__pyx_pf_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -7801,7 +7882,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__py goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -7810,18 +7891,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_7format_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_7format_format = {__Pyx_NAMESTR("format_format"), (PyCFunction)__pyx_pw_4cvcf_3VCF_7format_format, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_7format_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_7format_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_7format_format = {__Pyx_NAMESTR("format_format"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_7format_format, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_7format_format(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_fmt = 0; PyObject *__pyx_v_filter = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fmt,&__pyx_n_s__filter,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("format_format (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fmt,&__pyx_n_s__filter,0}; PyObject* values[3] = {0,0,0}; __pyx_defaults2 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults2, __pyx_self); values[2] = __pyx_dynamic_args->__pyx_arg_filter; @@ -7838,12 +7918,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_7format_format(PyObject *__pyx_self, PyObje kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fmt); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fmt)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -7873,16 +7951,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_7format_format(PyObject *__pyx_self, PyObje __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.format_format", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.format_format", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_6format_format(__pyx_self, __pyx_v_self, __pyx_v_fmt, __pyx_v_filter); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_6format_format(__pyx_self, __pyx_v_self, __pyx_v_fmt, __pyx_v_filter); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter) { PyObject *__pyx_v_values = NULL; PyObject *__pyx_v_nmb = NULL; PyObject *__pyx_v_format = NULL; @@ -7908,7 +7986,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py int __pyx_clineno = 0; __Pyx_RefNannySetupContext("format_format", 0); - /* "cvcf.pyx":417 + /* "pysam/cvcf.pyx":417 * * def format_format( self, fmt, filter=False ): * values = [('ID',fmt.id)] # <<<<<<<<<<<<<< @@ -7933,7 +8011,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __pyx_v_values = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":418 + /* "pysam/cvcf.pyx":418 * def format_format( self, fmt, filter=False ): * values = [('ID',fmt.id)] * if fmt.number != None and not filter: # <<<<<<<<<<<<<< @@ -7942,8 +8020,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -7956,7 +8033,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py } if (__pyx_t_4) { - /* "cvcf.pyx":419 + /* "pysam/cvcf.pyx":419 * values = [('ID',fmt.id)] * if fmt.number != None and not filter: * if fmt.numbertype == self.NT_UNKNOWN: nmb = "." # <<<<<<<<<<<<<< @@ -7967,8 +8044,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -7979,7 +8055,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py goto __pyx_L4; } - /* "cvcf.pyx":420 + /* "pysam/cvcf.pyx":420 * if fmt.number != None and not filter: * if fmt.numbertype == self.NT_UNKNOWN: nmb = "." * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) # <<<<<<<<<<<<<< @@ -7990,8 +8066,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_GOTREF(__pyx_t_6); __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8012,7 +8087,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py goto __pyx_L4; } - /* "cvcf.pyx":421 + /* "pysam/cvcf.pyx":421 * if fmt.numbertype == self.NT_UNKNOWN: nmb = "." * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" # <<<<<<<<<<<<<< @@ -8023,8 +8098,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8035,7 +8109,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py goto __pyx_L4; } - /* "cvcf.pyx":422 + /* "pysam/cvcf.pyx":422 * elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" # <<<<<<<<<<<<<< @@ -8046,8 +8120,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_GOTREF(__pyx_t_6); __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8058,7 +8131,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py goto __pyx_L4; } - /* "cvcf.pyx":423 + /* "pysam/cvcf.pyx":423 * elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" # <<<<<<<<<<<<<< @@ -8069,8 +8142,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8081,7 +8153,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py goto __pyx_L4; } - /* "cvcf.pyx":424 + /* "pysam/cvcf.pyx":424 * elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" * elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" # <<<<<<<<<<<<<< @@ -8092,8 +8164,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_GOTREF(__pyx_t_6); __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8105,7 +8176,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py } /*else*/ { - /* "cvcf.pyx":426 + /* "pysam/cvcf.pyx":426 * elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" * else: * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) # <<<<<<<<<<<<<< @@ -8131,7 +8202,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py } __pyx_L4:; - /* "cvcf.pyx":427 + /* "pysam/cvcf.pyx":427 * else: * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) * values.append( ('Number',nmb) ) # <<<<<<<<<<<<<< @@ -8149,7 +8220,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":428 + /* "pysam/cvcf.pyx":428 * raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) * values.append( ('Number',nmb) ) * values.append( ('Type', fmt.type) ) # <<<<<<<<<<<<<< @@ -8172,7 +8243,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py } __pyx_L3:; - /* "cvcf.pyx":429 + /* "pysam/cvcf.pyx":429 * values.append( ('Number',nmb) ) * values.append( ('Type', fmt.type) ) * values.append( ('Description', '"' + fmt.description + '"') ) # <<<<<<<<<<<<<< @@ -8198,7 +8269,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":430 + /* "pysam/cvcf.pyx":430 * values.append( ('Type', fmt.type) ) * values.append( ('Description', '"' + fmt.description + '"') ) * if self._version == 33: # <<<<<<<<<<<<<< @@ -8207,14 +8278,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_4) { - /* "cvcf.pyx":431 + /* "pysam/cvcf.pyx":431 * values.append( ('Description', '"' + fmt.description + '"') ) * if self._version == 33: * format = ",".join([v for k,v in values]) # <<<<<<<<<<<<<< @@ -8228,30 +8298,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __pyx_t_6 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_6); __pyx_t_8 = 0; for (;;) { if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_6)) break; - __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_6, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) { PyObject* sequence = __pyx_t_9; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) { - if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_10 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_11 = PyTuple_GET_ITEM(sequence, 1); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 2)) { - if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_10 = PyList_GET_ITEM(sequence, 0); __pyx_t_11 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_10); __Pyx_INCREF(__pyx_t_11); + #else + __pyx_t_10 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - } else { + } else + { Py_ssize_t index = -1; __pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_12); @@ -8262,12 +8342,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py index = 1; __pyx_t_11 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_11)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_11); if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_13 = NULL; __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; goto __pyx_L9_unpacking_done; __pyx_L8_unpacking_failed:; __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_13 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L9_unpacking_done:; } @@ -8277,7 +8358,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_XDECREF(__pyx_v_v); __pyx_v_v = __pyx_t_11; __pyx_t_11 = 0; - if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_v_v))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_v_v))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8296,7 +8377,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py } /*else*/ { - /* "cvcf.pyx":433 + /* "pysam/cvcf.pyx":433 * format = ",".join([v for k,v in values]) * else: * format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" # <<<<<<<<<<<<<< @@ -8310,30 +8391,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __pyx_t_2 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_2); __pyx_t_8 = 0; for (;;) { if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) { PyObject* sequence = __pyx_t_9; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) { - if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_11 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 2)) { - if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_11 = PyList_GET_ITEM(sequence, 0); __pyx_t_10 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_11); __Pyx_INCREF(__pyx_t_10); + #else + __pyx_t_11 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - } else { + } else + { Py_ssize_t index = -1; __pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_12); @@ -8344,12 +8435,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py index = 1; __pyx_t_10 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_10)) goto __pyx_L12_unpacking_failed; __Pyx_GOTREF(__pyx_t_10); if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_13 = NULL; __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; goto __pyx_L13_unpacking_done; __pyx_L12_unpacking_failed:; __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_13 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L13_unpacking_done:; } @@ -8370,7 +8462,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_10)); __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; - if (unlikely(PyList_Append(__pyx_t_6, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_PyList_Append(__pyx_t_6, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -8395,7 +8487,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py } __pyx_L5:; - /* "cvcf.pyx":434 + /* "pysam/cvcf.pyx":434 * else: * format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" * return format # <<<<<<<<<<<<<< @@ -8417,7 +8509,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py __Pyx_XDECREF(__pyx_t_10); __Pyx_XDECREF(__pyx_t_11); __Pyx_XDECREF(__pyx_t_12); - __Pyx_AddTraceback("cvcf.VCF.format_format", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.format_format", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_values); @@ -8431,19 +8523,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_9get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_9get_expected = {__Pyx_NAMESTR("get_expected"), (PyCFunction)__pyx_pw_4cvcf_3VCF_9get_expected, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_9get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_9get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_9get_expected = {__Pyx_NAMESTR("get_expected"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_9get_expected, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_9get_expected(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_format = 0; PyObject *__pyx_v_formatdict = 0; PyObject *__pyx_v_alt = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,&__pyx_n_s__formatdict,&__pyx_n_s__alt,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("get_expected (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,&__pyx_n_s__formatdict,&__pyx_n_s__alt,0}; PyObject* values[4] = {0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -8459,24 +8550,20 @@ static PyObject *__pyx_pw_4cvcf_3VCF_9get_expected(PyObject *__pyx_self, PyObjec kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt); - if (likely(values[3])) kw_args--; + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -8501,16 +8588,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_9get_expected(PyObject *__pyx_self, PyObjec __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.get_expected", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.get_expected", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_8get_expected(__pyx_self, __pyx_v_self, __pyx_v_format, __pyx_v_formatdict, __pyx_v_alt); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_8get_expected(__pyx_self, __pyx_v_self, __pyx_v_format, __pyx_v_formatdict, __pyx_v_alt); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":436 +/* "pysam/cvcf.pyx":436 * return format * * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<< @@ -8518,7 +8605,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_9get_expected(PyObject *__pyx_self, PyObjec * if fmt.numbertype == self.NT_UNKNOWN: return -1 */ -static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt) { PyObject *__pyx_v_fmt = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -8533,7 +8620,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_expected", 0); - /* "cvcf.pyx":437 + /* "pysam/cvcf.pyx":437 * * def get_expected(self, format, formatdict, alt): * fmt = formatdict[format] # <<<<<<<<<<<<<< @@ -8545,7 +8632,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __pyx_v_fmt = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":438 + /* "pysam/cvcf.pyx":438 * def get_expected(self, format, formatdict, alt): * fmt = formatdict[format] * if fmt.numbertype == self.NT_UNKNOWN: return -1 # <<<<<<<<<<<<<< @@ -8556,8 +8643,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8571,7 +8657,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx } __pyx_L3:; - /* "cvcf.pyx":439 + /* "pysam/cvcf.pyx":439 * fmt = formatdict[format] * if fmt.numbertype == self.NT_UNKNOWN: return -1 * if fmt.numbertype == self.NT_NUMBER: return fmt.number # <<<<<<<<<<<<<< @@ -8582,8 +8668,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8599,7 +8684,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx } __pyx_L4:; - /* "cvcf.pyx":440 + /* "pysam/cvcf.pyx":440 * if fmt.numbertype == self.NT_UNKNOWN: return -1 * if fmt.numbertype == self.NT_NUMBER: return fmt.number * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 # <<<<<<<<<<<<<< @@ -8610,8 +8695,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8628,7 +8712,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx } __pyx_L5:; - /* "cvcf.pyx":441 + /* "pysam/cvcf.pyx":441 * if fmt.numbertype == self.NT_NUMBER: return fmt.number * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) # <<<<<<<<<<<<<< @@ -8639,8 +8723,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8657,7 +8740,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx } __pyx_L6:; - /* "cvcf.pyx":442 + /* "pysam/cvcf.pyx":442 * if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 # <<<<<<<<<<<<<< @@ -8668,8 +8751,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8687,7 +8769,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx } __pyx_L7:; - /* "cvcf.pyx":443 + /* "pysam/cvcf.pyx":443 * if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) # <<<<<<<<<<<<<< @@ -8698,8 +8780,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -8717,7 +8798,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx } __pyx_L8:; - /* "cvcf.pyx":444 + /* "pysam/cvcf.pyx":444 * if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 * if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) * return 0 # <<<<<<<<<<<<<< @@ -8735,7 +8816,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("cvcf.VCF.get_expected", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.get_expected", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_fmt); @@ -8745,20 +8826,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_11_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_11_add_definition = {__Pyx_NAMESTR("_add_definition"), (PyCFunction)__pyx_pw_4cvcf_3VCF_11_add_definition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_11_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_11_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_11_add_definition = {__Pyx_NAMESTR("_add_definition"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_11_add_definition, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_11_add_definition(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_formatdict = 0; PyObject *__pyx_v_key = 0; PyObject *__pyx_v_data = 0; PyObject *__pyx_v_line = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__formatdict,&__pyx_n_s__key,&__pyx_n_s__data,&__pyx_n_s__line,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("_add_definition (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__formatdict,&__pyx_n_s__key,&__pyx_n_s__data,&__pyx_n_s__line,0}; PyObject* values[5] = {0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -8775,30 +8855,25 @@ static PyObject *__pyx_pw_4cvcf_3VCF_11_add_definition(PyObject *__pyx_self, PyO kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data); - if (likely(values[3])) kw_args--; + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: - values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[4])) kw_args--; + if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -8825,16 +8900,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_11_add_definition(PyObject *__pyx_self, PyO __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF._add_definition", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF._add_definition", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_10_add_definition(__pyx_self, __pyx_v_self, __pyx_v_formatdict, __pyx_v_key, __pyx_v_data, __pyx_v_line); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(__pyx_self, __pyx_v_self, __pyx_v_formatdict, __pyx_v_key, __pyx_v_data, __pyx_v_line); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":447 +/* "pysam/cvcf.pyx":447 * * * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<< @@ -8842,7 +8917,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_11_add_definition(PyObject *__pyx_self, PyO * self.error(line,self.ERROR_UNKNOWN_KEY,key) */ -static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -8855,14 +8930,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ __Pyx_RefNannySetupContext("_add_definition", 0); __Pyx_INCREF(__pyx_v_data); - /* "cvcf.pyx":448 + /* "pysam/cvcf.pyx":448 * * def _add_definition(self, formatdict, key, data, line ): * if key in formatdict: return # <<<<<<<<<<<<<< * self.error(line,self.ERROR_UNKNOWN_KEY,key) * if data == None: */ - __pyx_t_1 = ((PySequence_Contains(__pyx_v_formatdict, __pyx_v_key))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_v_formatdict, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { __Pyx_XDECREF(__pyx_r); __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -8871,7 +8946,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ } __pyx_L3:; - /* "cvcf.pyx":449 + /* "pysam/cvcf.pyx":449 * def _add_definition(self, formatdict, key, data, line ): * if key in formatdict: return * self.error(line,self.ERROR_UNKNOWN_KEY,key) # <<<<<<<<<<<<<< @@ -8899,20 +8974,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":450 + /* "pysam/cvcf.pyx":450 * if key in formatdict: return * self.error(line,self.ERROR_UNKNOWN_KEY,key) * if data == None: # <<<<<<<<<<<<<< * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") * return */ - __pyx_t_3 = PyObject_RichCompare(__pyx_v_data, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_data, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_1) { - /* "cvcf.pyx":451 + /* "pysam/cvcf.pyx":451 * self.error(line,self.ERROR_UNKNOWN_KEY,key) * if data == None: * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") # <<<<<<<<<<<<<< @@ -8950,7 +9024,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":452 + /* "pysam/cvcf.pyx":452 * if data == None: * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") * return # <<<<<<<<<<<<<< @@ -8964,7 +9038,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ } __pyx_L4:; - /* "cvcf.pyx":453 + /* "pysam/cvcf.pyx":453 * formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") * return * if data == []: data = [""] # unsure what type -- say string # <<<<<<<<<<<<<< @@ -8973,8 +9047,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ */ __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_2 = PyObject_RichCompare(__pyx_v_data, ((PyObject *)__pyx_t_4), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_data, ((PyObject *)__pyx_t_4), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -8991,7 +9064,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ } __pyx_L5:; - /* "cvcf.pyx":454 + /* "pysam/cvcf.pyx":454 * return * if data == []: data = [""] # unsure what type -- say string * if type(data[0]) == type(0.0): # <<<<<<<<<<<<<< @@ -9002,15 +9075,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ __Pyx_GOTREF(__pyx_t_2); __pyx_t_4 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_2)), ((PyObject *)Py_TYPE(__pyx_t_4)), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_2)), ((PyObject *)Py_TYPE(__pyx_t_4)), Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_1) { - /* "cvcf.pyx":455 + /* "pysam/cvcf.pyx":455 * if data == []: data = [""] # unsure what type -- say string * if type(data[0]) == type(0.0): * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) # <<<<<<<<<<<<<< @@ -9048,7 +9120,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":456 + /* "pysam/cvcf.pyx":456 * if type(data[0]) == type(0.0): * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) * return # <<<<<<<<<<<<<< @@ -9062,7 +9134,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ } __pyx_L6:; - /* "cvcf.pyx":457 + /* "pysam/cvcf.pyx":457 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) * return * if type(data[0]) == type(0): # <<<<<<<<<<<<<< @@ -9071,14 +9143,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ */ __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_data, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_2 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_4)), ((PyObject *)Py_TYPE(__pyx_int_0)), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_4)), ((PyObject *)Py_TYPE(__pyx_int_0)), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_1) { - /* "cvcf.pyx":458 + /* "pysam/cvcf.pyx":458 * return * if type(data[0]) == type(0): * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) # <<<<<<<<<<<<<< @@ -9116,7 +9187,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":459 + /* "pysam/cvcf.pyx":459 * if type(data[0]) == type(0): * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) * return # <<<<<<<<<<<<<< @@ -9130,7 +9201,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ } __pyx_L7:; - /* "cvcf.pyx":460 + /* "pysam/cvcf.pyx":460 * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) * return * formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".") # <<<<<<<<<<<<<< @@ -9174,7 +9245,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); - __Pyx_AddTraceback("cvcf.VCF._add_definition", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF._add_definition", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_data); @@ -9183,7 +9254,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ return __pyx_r; } -/* "cvcf.pyx":464 +/* "pysam/cvcf.pyx":464 * * # todo: trim trailing missing values * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<< @@ -9191,7 +9262,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *_ * if type(data) == type([]): # for FORMAT field, make data with dummy values */ -static PyObject *__pyx_pf_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -9219,7 +9290,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__py goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -9228,21 +9299,20 @@ static PyObject *__pyx_pf_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_13format_formatdata = {__Pyx_NAMESTR("format_formatdata"), (PyCFunction)__pyx_pw_4cvcf_3VCF_13format_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_13format_formatdata = {__Pyx_NAMESTR("format_formatdata"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_13format_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_data = 0; PyObject *__pyx_v_format = 0; PyObject *__pyx_v_key = 0; PyObject *__pyx_v_value = 0; PyObject *__pyx_v_separator = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__data,&__pyx_n_s__format,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__separator,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("format_formatdata (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__data,&__pyx_n_s__format,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__separator,0}; PyObject* values[6] = {0,0,0,0,0,0}; __pyx_defaults3 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_self); values[3] = __pyx_dynamic_args->__pyx_arg_key; @@ -9264,18 +9334,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_self, P kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -9321,16 +9388,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_self, P __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.format_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.format_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_12format_formatdata(__pyx_self, __pyx_v_self, __pyx_v_data, __pyx_v_format, __pyx_v_key, __pyx_v_value, __pyx_v_separator); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(__pyx_self, __pyx_v_self, __pyx_v_data, __pyx_v_format, __pyx_v_key, __pyx_v_value, __pyx_v_separator); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator) { PyObject *__pyx_v_output = NULL; PyObject *__pyx_v_sdata = NULL; PyObject *__pyx_v_d = NULL; @@ -9360,7 +9427,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __Pyx_RefNannySetupContext("format_formatdata", 0); __Pyx_INCREF(__pyx_v_data); - /* "cvcf.pyx":465 + /* "pysam/cvcf.pyx":465 * # todo: trim trailing missing values * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): * output, sdata = [], [] # <<<<<<<<<<<<<< @@ -9376,7 +9443,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_v_sdata = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":466 + /* "pysam/cvcf.pyx":466 * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): * output, sdata = [], [] * if type(data) == type([]): # for FORMAT field, make data with dummy values # <<<<<<<<<<<<<< @@ -9385,14 +9452,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(((PyObject *)__pyx_t_2))), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(((PyObject *)__pyx_t_2))), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":467 + /* "pysam/cvcf.pyx":467 * output, sdata = [], [] * if type(data) == type([]): # for FORMAT field, make data with dummy values * d = {} # <<<<<<<<<<<<<< @@ -9404,7 +9470,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_v_d = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":468 + /* "pysam/cvcf.pyx":468 * if type(data) == type([]): # for FORMAT field, make data with dummy values * d = {} * for k in data: d[k] = [] # <<<<<<<<<<<<<< @@ -9422,10 +9488,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject for (;;) { if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_2 = __pyx_t_5(__pyx_t_1); if (unlikely(!__pyx_t_2)) { @@ -9447,7 +9521,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":469 + /* "pysam/cvcf.pyx":469 * d = {} * for k in data: d[k] = [] * data = d # <<<<<<<<<<<<<< @@ -9461,7 +9535,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __pyx_L3:; - /* "cvcf.pyx":471 + /* "pysam/cvcf.pyx":471 * data = d * # convert missing values; and silently add definitions if required * for k in data: # <<<<<<<<<<<<<< @@ -9479,10 +9553,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject for (;;) { if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_2 = __pyx_t_5(__pyx_t_1); if (unlikely(!__pyx_t_2)) { @@ -9498,7 +9580,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_v_k = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":472 + /* "pysam/cvcf.pyx":472 * # convert missing values; and silently add definitions if required * for k in data: * self._add_definition( format, k, data[k], "(output)" ) # <<<<<<<<<<<<<< @@ -9529,7 +9611,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "cvcf.pyx":473 + /* "pysam/cvcf.pyx":473 * for k in data: * self._add_definition( format, k, data[k], "(output)" ) * for idx,v in enumerate(data[k]): # <<<<<<<<<<<<<< @@ -9552,10 +9634,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject for (;;) { if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_2)) break; - __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_7 = __pyx_t_9(__pyx_t_2); if (unlikely(!__pyx_t_7)) { @@ -9579,7 +9669,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_t_6 = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":474 + /* "pysam/cvcf.pyx":474 * self._add_definition( format, k, data[k], "(output)" ) * for idx,v in enumerate(data[k]): * if v == format[k].missingvalue: data[k][idx] = "." # <<<<<<<<<<<<<< @@ -9591,8 +9681,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_t_10 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, __pyx_t_10, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, __pyx_t_10, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -9610,7 +9699,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":476 + /* "pysam/cvcf.pyx":476 * if v == format[k].missingvalue: data[k][idx] = "." * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string * for k in data: # <<<<<<<<<<<<<< @@ -9628,10 +9717,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject for (;;) { if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_6 = __pyx_t_5(__pyx_t_1); if (unlikely(!__pyx_t_6)) { @@ -9647,14 +9744,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_v_k = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":477 + /* "pysam/cvcf.pyx":477 * # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string * for k in data: * if k != 'GT': sdata.append( (k,data[k]) ) # <<<<<<<<<<<<<< * sdata.sort() * if 'GT' in data: */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_k, ((PyObject *)__pyx_n_s__GT), Py_NE); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_RichCompare(__pyx_v_k, ((PyObject *)__pyx_n_s__GT), Py_NE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (__pyx_t_3) { __pyx_t_6 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); @@ -9674,7 +9773,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":478 + /* "pysam/cvcf.pyx":478 * for k in data: * if k != 'GT': sdata.append( (k,data[k]) ) * sdata.sort() # <<<<<<<<<<<<<< @@ -9683,17 +9782,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject */ __pyx_t_11 = PyList_Sort(((PyObject *)__pyx_v_sdata)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 478; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":479 + /* "pysam/cvcf.pyx":479 * if k != 'GT': sdata.append( (k,data[k]) ) * sdata.sort() * if 'GT' in data: # <<<<<<<<<<<<<< * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata * for k,v in sdata: */ - __pyx_t_3 = ((PySequence_Contains(__pyx_v_data, ((PyObject *)__pyx_n_s__GT)))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__GT), __pyx_v_data, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_3) { - /* "cvcf.pyx":480 + /* "pysam/cvcf.pyx":480 * sdata.sort() * if 'GT' in data: * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata # <<<<<<<<<<<<<< @@ -9738,7 +9837,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __pyx_L14:; - /* "cvcf.pyx":481 + /* "pysam/cvcf.pyx":481 * if 'GT' in data: * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata * for k,v in sdata: # <<<<<<<<<<<<<< @@ -9748,30 +9847,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_t_6 = ((PyObject *)__pyx_v_sdata); __Pyx_INCREF(__pyx_t_6); __pyx_t_4 = 0; for (;;) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_6)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_6, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) { PyObject* sequence = __pyx_t_2; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) { - if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_7 = PyTuple_GET_ITEM(sequence, 1); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 2)) { - if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyList_GET_ITEM(sequence, 0); __pyx_t_7 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_1); __Pyx_INCREF(__pyx_t_7); + #else + __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - } else { + } else + { Py_ssize_t index = -1; __pyx_t_10 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); @@ -9782,12 +9891,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject index = 1; __pyx_t_7 = __pyx_t_12(__pyx_t_10); if (unlikely(!__pyx_t_7)) goto __pyx_L17_unpacking_failed; __Pyx_GOTREF(__pyx_t_7); if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = NULL; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; goto __pyx_L18_unpacking_done; __pyx_L17_unpacking_failed:; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_12 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L18_unpacking_done:; } @@ -9798,7 +9908,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_v_v = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":482 + /* "pysam/cvcf.pyx":482 * sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata * for k,v in sdata: * if v == []: v = None # <<<<<<<<<<<<<< @@ -9807,8 +9917,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -9820,7 +9929,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __pyx_L19:; - /* "cvcf.pyx":483 + /* "pysam/cvcf.pyx":483 * for k,v in sdata: * if v == []: v = None * if key and value: # <<<<<<<<<<<<<< @@ -9836,15 +9945,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } if (__pyx_t_14) { - /* "cvcf.pyx":484 + /* "pysam/cvcf.pyx":484 * if v == []: v = None * if key and value: * if v != None: output.append( k+"="+','.join(map(str,v)) ) # <<<<<<<<<<<<<< * else: output.append( k ) * elif key: output.append(k) */ - __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (__pyx_t_14) { @@ -9882,7 +9990,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } /*else*/ { - /* "cvcf.pyx":485 + /* "pysam/cvcf.pyx":485 * if key and value: * if v != None: output.append( k+"="+','.join(map(str,v)) ) * else: output.append( k ) # <<<<<<<<<<<<<< @@ -9895,7 +10003,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject goto __pyx_L20; } - /* "cvcf.pyx":486 + /* "pysam/cvcf.pyx":486 * if v != None: output.append( k+"="+','.join(map(str,v)) ) * else: output.append( k ) * elif key: output.append(k) # <<<<<<<<<<<<<< @@ -9908,7 +10016,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject goto __pyx_L20; } - /* "cvcf.pyx":487 + /* "pysam/cvcf.pyx":487 * else: output.append( k ) * elif key: output.append(k) * elif value: # <<<<<<<<<<<<<< @@ -9918,15 +10026,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_value); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_14) { - /* "cvcf.pyx":488 + /* "pysam/cvcf.pyx":488 * elif key: output.append(k) * elif value: * if v != None: output.append( ','.join(map(str,v)) ) # <<<<<<<<<<<<<< * else: output.append( "." ) # should not happen * # snip off trailing missing data */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_14) { @@ -9958,7 +10065,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } /*else*/ { - /* "cvcf.pyx":489 + /* "pysam/cvcf.pyx":489 * elif value: * if v != None: output.append( ','.join(map(str,v)) ) * else: output.append( "." ) # should not happen # <<<<<<<<<<<<<< @@ -9977,7 +10084,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "cvcf.pyx":491 + /* "pysam/cvcf.pyx":491 * else: output.append( "." ) # should not happen * # snip off trailing missing data * while len(output) > 1: # <<<<<<<<<<<<<< @@ -9986,19 +10093,24 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject */ while (1) { if (unlikely(((PyObject *)__pyx_v_output) == Py_None)) { - PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_4 = PyList_GET_SIZE(((PyObject *)__pyx_v_output)); + __pyx_t_4 = PyList_GET_SIZE(((PyObject *)__pyx_v_output)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = (__pyx_t_4 > 1); if (!__pyx_t_14) break; - /* "cvcf.pyx":492 + /* "pysam/cvcf.pyx":492 * # snip off trailing missing data * while len(output) > 1: * last = output[-1].replace(',','').replace('.','') # <<<<<<<<<<<<<< * if len(last)>0: break * output = output[:-1] */ + if (unlikely(((PyObject *)__pyx_v_output) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable"); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_6 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_output), -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__replace); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -10017,7 +10129,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __pyx_v_last = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":493 + /* "pysam/cvcf.pyx":493 * while len(output) > 1: * last = output[-1].replace(',','').replace('.','') * if len(last)>0: break # <<<<<<<<<<<<<< @@ -10032,7 +10144,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __pyx_L25:; - /* "cvcf.pyx":494 + /* "pysam/cvcf.pyx":494 * last = output[-1].replace(',','').replace('.','') * if len(last)>0: break * output = output[:-1] # <<<<<<<<<<<<<< @@ -10047,7 +10159,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } __pyx_L24_break:; - /* "cvcf.pyx":495 + /* "pysam/cvcf.pyx":495 * if len(last)>0: break * output = output[:-1] * return separator.join(output) # <<<<<<<<<<<<<< @@ -10078,7 +10190,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_7); __Pyx_XDECREF(__pyx_t_10); - __Pyx_AddTraceback("cvcf.VCF.format_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.format_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_output); @@ -10095,19 +10207,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_15enter_default_format(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_15enter_default_format = {__Pyx_NAMESTR("enter_default_format"), (PyCFunction)__pyx_pw_4cvcf_3VCF_15enter_default_format, METH_O, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_15enter_default_format(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_15enter_default_format(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_15enter_default_format = {__Pyx_NAMESTR("enter_default_format"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_15enter_default_format, METH_O, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_15enter_default_format(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("enter_default_format (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_4cvcf_3VCF_14enter_default_format(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":498 +/* "pysam/cvcf.pyx":498 * * * def enter_default_format(self): # <<<<<<<<<<<<<< @@ -10115,7 +10226,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_15enter_default_format(PyObject *__pyx_self * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), */ -static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_v_f = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -10142,7 +10253,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje int __pyx_clineno = 0; __Pyx_RefNannySetupContext("enter_default_format", 0); - /* "cvcf.pyx":499 + /* "pysam/cvcf.pyx":499 * * def enter_default_format(self): * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), # <<<<<<<<<<<<<< @@ -10178,7 +10289,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "cvcf.pyx":500 + /* "pysam/cvcf.pyx":500 * def enter_default_format(self): * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), # <<<<<<<<<<<<<< @@ -10214,7 +10325,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; - /* "cvcf.pyx":501 + /* "pysam/cvcf.pyx":501 * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), # <<<<<<<<<<<<<< @@ -10250,7 +10361,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; - /* "cvcf.pyx":502 + /* "pysam/cvcf.pyx":502 * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), # <<<<<<<<<<<<<< @@ -10286,7 +10397,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - /* "cvcf.pyx":503 + /* "pysam/cvcf.pyx":503 * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), # <<<<<<<<<<<<<< @@ -10322,7 +10433,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; - /* "cvcf.pyx":504 + /* "pysam/cvcf.pyx":504 * FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), # <<<<<<<<<<<<<< @@ -10358,7 +10469,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - /* "cvcf.pyx":505 + /* "pysam/cvcf.pyx":505 * FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'), # <<<<<<<<<<<<<< @@ -10394,7 +10505,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; - /* "cvcf.pyx":506 + /* "pysam/cvcf.pyx":506 * FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'), * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'), # <<<<<<<<<<<<<< @@ -10430,7 +10541,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - /* "cvcf.pyx":507 + /* "pysam/cvcf.pyx":507 * FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'), * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'), * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'), # <<<<<<<<<<<<<< @@ -10466,7 +10577,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0; - /* "cvcf.pyx":508 + /* "pysam/cvcf.pyx":508 * FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'), * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'), * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid # <<<<<<<<<<<<<< @@ -10502,7 +10613,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0; - /* "cvcf.pyx":509 + /* "pysam/cvcf.pyx":509 * FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'), * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'), # <<<<<<<<<<<<<< @@ -10538,7 +10649,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0; - /* "cvcf.pyx":510 + /* "pysam/cvcf.pyx":510 * FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'), * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1), # <<<<<<<<<<<<<< @@ -10574,7 +10685,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0; - /* "cvcf.pyx":511 + /* "pysam/cvcf.pyx":511 * FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'), * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1), * FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1), # <<<<<<<<<<<<<< @@ -10610,7 +10721,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0; - /* "cvcf.pyx":512 + /* "pysam/cvcf.pyx":512 * FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1), * FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1), * FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1), # <<<<<<<<<<<<<< @@ -10693,7 +10804,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_DECREF(((PyObject *)__pyx_t_16)); __pyx_t_16 = 0; for (;;) { - /* "cvcf.pyx":499 + /* "pysam/cvcf.pyx":499 * * def enter_default_format(self): * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), # <<<<<<<<<<<<<< @@ -10701,12 +10812,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje * FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), */ if (__pyx_t_17 >= PyList_GET_SIZE(__pyx_t_14)) break; - __pyx_t_16 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_17); __Pyx_INCREF(__pyx_t_16); __pyx_t_17++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_16 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_17); __Pyx_INCREF(__pyx_t_16); __pyx_t_17++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_16 = PySequence_ITEM(__pyx_t_14, __pyx_t_17); __pyx_t_17++; if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif __Pyx_XDECREF(__pyx_v_f); __pyx_v_f = __pyx_t_16; __pyx_t_16 = 0; - /* "cvcf.pyx":514 + /* "pysam/cvcf.pyx":514 * FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1), * ]: * if f.id not in self._format: # <<<<<<<<<<<<<< @@ -10717,12 +10832,12 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_GOTREF(__pyx_t_16); __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_13); - __pyx_t_18 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_13, __pyx_t_16))); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_18 = (__Pyx_PySequence_Contains(__pyx_t_16, __pyx_t_13, Py_NE)); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0; __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; if (__pyx_t_18) { - /* "cvcf.pyx":515 + /* "pysam/cvcf.pyx":515 * ]: * if f.id not in self._format: * self._format[f.id] = f # <<<<<<<<<<<<<< @@ -10761,7 +10876,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje __Pyx_XDECREF(__pyx_t_14); __Pyx_XDECREF(__pyx_t_15); __Pyx_XDECREF(__pyx_t_16); - __Pyx_AddTraceback("cvcf.VCF.enter_default_format", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.enter_default_format", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_f); @@ -10771,17 +10886,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObje } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_17parse_header = {__Pyx_NAMESTR("parse_header"), (PyCFunction)__pyx_pw_4cvcf_3VCF_17parse_header, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_17parse_header = {__Pyx_NAMESTR("parse_header"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_17parse_header, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_line = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("parse_header (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -10795,12 +10909,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObje kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -10821,16 +10933,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObje __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_16parse_header(__pyx_self, __pyx_v_self, __pyx_v_line); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_16parse_header(__pyx_self, __pyx_v_self, __pyx_v_line); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":517 +/* "pysam/cvcf.pyx":517 * self._format[f.id] = f * * def parse_header( self, line ): # <<<<<<<<<<<<<< @@ -10838,7 +10950,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObje * elts = line[2:].split('=') */ -static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line) { PyObject *__pyx_v_elts = NULL; PyObject *__pyx_v_key = NULL; PyObject *__pyx_v_value = NULL; @@ -10855,7 +10967,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py int __pyx_clineno = 0; __Pyx_RefNannySetupContext("parse_header", 0); - /* "cvcf.pyx":518 + /* "pysam/cvcf.pyx":518 * * def parse_header( self, line ): * assert line.startswith('##') # <<<<<<<<<<<<<< @@ -10876,7 +10988,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py } #endif - /* "cvcf.pyx":519 + /* "pysam/cvcf.pyx":519 * def parse_header( self, line ): * assert line.startswith('##') * elts = line[2:].split('=') # <<<<<<<<<<<<<< @@ -10894,7 +11006,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py __pyx_v_elts = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":520 + /* "pysam/cvcf.pyx":520 * assert line.startswith('##') * elts = line[2:].split('=') * key = elts[0].strip() # <<<<<<<<<<<<<< @@ -10912,7 +11024,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py __pyx_v_key = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":521 + /* "pysam/cvcf.pyx":521 * elts = line[2:].split('=') * key = elts[0].strip() * value = '='.join(elts[1:]).strip() # <<<<<<<<<<<<<< @@ -10941,27 +11053,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py __pyx_v_value = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":522 + /* "pysam/cvcf.pyx":522 * key = elts[0].strip() * value = '='.join(elts[1:]).strip() * if key == "fileformat": # <<<<<<<<<<<<<< * if value == "VCFv3.3": * self._version = 33 */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__fileformat), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__fileformat), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":523 + /* "pysam/cvcf.pyx":523 * value = '='.join(elts[1:]).strip() * if key == "fileformat": * if value == "VCFv3.3": # <<<<<<<<<<<<<< * self._version = 33 * elif value == "VCFv4.0": */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_79), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_79), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":524 + /* "pysam/cvcf.pyx":524 * if key == "fileformat": * if value == "VCFv3.3": * self._version = 33 # <<<<<<<<<<<<<< @@ -10972,17 +11088,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py goto __pyx_L4; } - /* "cvcf.pyx":525 + /* "pysam/cvcf.pyx":525 * if value == "VCFv3.3": * self._version = 33 * elif value == "VCFv4.0": # <<<<<<<<<<<<<< * self._version = 40 * elif value == "VCFv4.1": */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_80), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_80), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":526 + /* "pysam/cvcf.pyx":526 * self._version = 33 * elif value == "VCFv4.0": * self._version = 40 # <<<<<<<<<<<<<< @@ -10993,17 +11111,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py goto __pyx_L4; } - /* "cvcf.pyx":527 + /* "pysam/cvcf.pyx":527 * elif value == "VCFv4.0": * self._version = 40 * elif value == "VCFv4.1": # <<<<<<<<<<<<<< * # AH - for testing * self._version = 40 */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_81), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_81), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":529 + /* "pysam/cvcf.pyx":529 * elif value == "VCFv4.1": * # AH - for testing * self._version = 40 # <<<<<<<<<<<<<< @@ -11015,7 +11135,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py } /*else*/ { - /* "cvcf.pyx":531 + /* "pysam/cvcf.pyx":531 * self._version = 40 * else: * self.error(line,self.UNKNOWN_FORMAT_STRING) # <<<<<<<<<<<<<< @@ -11044,17 +11164,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py goto __pyx_L3; } - /* "cvcf.pyx":532 + /* "pysam/cvcf.pyx":532 * else: * self.error(line,self.UNKNOWN_FORMAT_STRING) * elif key == "INFO": # <<<<<<<<<<<<<< * f = self.parse_format(line, value) * self._info[ f.id ] = f */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__INFO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__INFO), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":533 + /* "pysam/cvcf.pyx":533 * self.error(line,self.UNKNOWN_FORMAT_STRING) * elif key == "INFO": * f = self.parse_format(line, value) # <<<<<<<<<<<<<< @@ -11078,7 +11200,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py __pyx_v_f = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":534 + /* "pysam/cvcf.pyx":534 * elif key == "INFO": * f = self.parse_format(line, value) * self._info[ f.id ] = f # <<<<<<<<<<<<<< @@ -11095,17 +11217,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py goto __pyx_L3; } - /* "cvcf.pyx":535 + /* "pysam/cvcf.pyx":535 * f = self.parse_format(line, value) * self._info[ f.id ] = f * elif key == "FILTER": # <<<<<<<<<<<<<< * f = self.parse_format(line, value, filter=True) * self._filter[ f.id ] = f */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":536 + /* "pysam/cvcf.pyx":536 * self._info[ f.id ] = f * elif key == "FILTER": * f = self.parse_format(line, value, filter=True) # <<<<<<<<<<<<<< @@ -11136,7 +11260,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py __pyx_v_f = __pyx_t_5; __pyx_t_5 = 0; - /* "cvcf.pyx":537 + /* "pysam/cvcf.pyx":537 * elif key == "FILTER": * f = self.parse_format(line, value, filter=True) * self._filter[ f.id ] = f # <<<<<<<<<<<<<< @@ -11153,17 +11277,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py goto __pyx_L3; } - /* "cvcf.pyx":538 + /* "pysam/cvcf.pyx":538 * f = self.parse_format(line, value, filter=True) * self._filter[ f.id ] = f * elif key == "FORMAT": # <<<<<<<<<<<<<< * f = self.parse_format(line, value) * self._format[ f.id ] = f */ - __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__FORMAT), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__FORMAT), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_3) { - /* "cvcf.pyx":539 + /* "pysam/cvcf.pyx":539 * self._filter[ f.id ] = f * elif key == "FORMAT": * f = self.parse_format(line, value) # <<<<<<<<<<<<<< @@ -11187,7 +11313,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py __pyx_v_f = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":540 + /* "pysam/cvcf.pyx":540 * elif key == "FORMAT": * f = self.parse_format(line, value) * self._format[ f.id ] = f # <<<<<<<<<<<<<< @@ -11205,7 +11331,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py } /*else*/ { - /* "cvcf.pyx":543 + /* "pysam/cvcf.pyx":543 * else: * # keep other keys in the header field * self._header.append( (key,value) ) # <<<<<<<<<<<<<< @@ -11237,7 +11363,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); - __Pyx_AddTraceback("cvcf.VCF.parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_elts); @@ -11250,17 +11376,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_19write_header = {__Pyx_NAMESTR("write_header"), (PyCFunction)__pyx_pw_4cvcf_3VCF_19write_header, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_19write_header = {__Pyx_NAMESTR("write_header"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_19write_header, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("write_header (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -11274,12 +11399,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObje kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -11300,16 +11423,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObje __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_18write_header(__pyx_self, __pyx_v_self, __pyx_v_stream); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_18write_header(__pyx_self, __pyx_v_self, __pyx_v_stream); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":546 +/* "pysam/cvcf.pyx":546 * * * def write_header( self, stream ): # <<<<<<<<<<<<<< @@ -11317,7 +11440,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObje * for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) */ -static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { PyObject *__pyx_v_key = NULL; PyObject *__pyx_v_value = NULL; PyObject *__pyx_v_var = NULL; @@ -11334,15 +11457,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py PyObject *__pyx_t_7 = NULL; PyObject *(*__pyx_t_8)(PyObject *); Py_ssize_t __pyx_t_9; - PyObject *__pyx_t_10 = NULL; + Py_ssize_t __pyx_t_10; int __pyx_t_11; - PyObject *__pyx_t_12 = NULL; + int __pyx_t_12; + PyObject *__pyx_t_13 = NULL; + PyObject *__pyx_t_14 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("write_header", 0); - /* "cvcf.pyx":547 + /* "pysam/cvcf.pyx":547 * * def write_header( self, stream ): * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) # <<<<<<<<<<<<<< @@ -11383,7 +11508,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":548 + /* "pysam/cvcf.pyx":548 * def write_header( self, stream ): * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) * for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) # <<<<<<<<<<<<<< @@ -11404,10 +11529,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py for (;;) { if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break; - __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_4 = __pyx_t_6(__pyx_t_2); if (unlikely(!__pyx_t_4)) { @@ -11421,27 +11554,33 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py } if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) { PyObject* sequence = __pyx_t_4; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) { - if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_3 = PyTuple_GET_ITEM(sequence, 1); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 2)) { - if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_1 = PyList_GET_ITEM(sequence, 0); __pyx_t_3 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_1); __Pyx_INCREF(__pyx_t_3); + #else + __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - } else { + } else + { Py_ssize_t index = -1; __pyx_t_7 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); @@ -11452,12 +11591,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py index = 1; __pyx_t_3 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed; __Pyx_GOTREF(__pyx_t_3); if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = NULL; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; goto __pyx_L6_unpacking_done; __pyx_L5_unpacking_failed:; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_8 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L6_unpacking_done:; } @@ -11493,7 +11633,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":549 + /* "pysam/cvcf.pyx":549 * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) * for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) * for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: # <<<<<<<<<<<<<< @@ -11545,30 +11685,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; for (;;) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) { PyObject* sequence = __pyx_t_2; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) { - if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_1 = PyTuple_GET_ITEM(sequence, 1); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 2)) { - if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } __pyx_t_3 = PyList_GET_ITEM(sequence, 0); __pyx_t_1 = PyList_GET_ITEM(sequence, 1); } __Pyx_INCREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_1); + #else + __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - } else { + } else + { Py_ssize_t index = -1; __pyx_t_7 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); @@ -11579,12 +11729,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py index = 1; __pyx_t_1 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_1)) goto __pyx_L9_unpacking_failed; __Pyx_GOTREF(__pyx_t_1); if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = NULL; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; goto __pyx_L10_unpacking_done; __pyx_L9_unpacking_failed:; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __pyx_t_8 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L10_unpacking_done:; } @@ -11595,45 +11746,28 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py __pyx_v_label = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":550 + /* "pysam/cvcf.pyx":550 * for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) * for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: * for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER")))) # <<<<<<<<<<<<<< * * */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_var, __pyx_n_s__itervalues); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) { - __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_9 = 0; - __pyx_t_6 = NULL; - } else { - __pyx_t_9 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_6 = Py_TYPE(__pyx_t_2)->tp_iternext; + __pyx_t_9 = 0; + if (unlikely(__pyx_v_var == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues"); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - for (;;) { - if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) { - if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++; - } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) { - if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_2)) break; - __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++; - } else { - __pyx_t_1 = __pyx_t_6(__pyx_t_2); - if (unlikely(!__pyx_t_1)) { - if (PyErr_Occurred()) { - if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); - else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } - break; - } - __Pyx_GOTREF(__pyx_t_1); - } + __pyx_t_1 = __Pyx_dict_iterator(__pyx_v_var, 0, ((PyObject *)__pyx_n_s__itervalues), (&__pyx_t_10), (&__pyx_t_11)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); + __pyx_t_2 = __pyx_t_1; + __pyx_t_1 = 0; + while (1) { + __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_2, __pyx_t_10, &__pyx_t_9, NULL, &__pyx_t_1, NULL, __pyx_t_11); + if (unlikely(__pyx_t_12 == 0)) break; + if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_XDECREF(__pyx_v_f); __pyx_v_f = __pyx_t_1; __pyx_t_1 = 0; @@ -11646,39 +11780,37 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py __Pyx_INCREF(__pyx_v_f); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_f); __Pyx_GIVEREF(__pyx_v_f); - __pyx_t_10 = PyDict_New(); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_10)); - __pyx_t_11 = __Pyx_PyString_Equals(__pyx_v_label, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_12 = __Pyx_PyBool_FromLong(__pyx_t_11); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_12); - if (PyDict_SetItem(__pyx_t_10, ((PyObject *)__pyx_n_s__filter), __pyx_t_12) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; - __pyx_t_12 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_12); + __pyx_t_13 = PyDict_New(); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_13)); + __pyx_t_14 = PyObject_RichCompare(__pyx_v_label, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_13, ((PyObject *)__pyx_n_s__filter), __pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; + __pyx_t_14 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_14); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0; + __pyx_t_13 = PyTuple_New(2); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_13); __Pyx_INCREF(__pyx_v_label); - PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_label); + PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_v_label); __Pyx_GIVEREF(__pyx_v_label); - PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_12); - __Pyx_GIVEREF(__pyx_t_12); - __pyx_t_12 = 0; - __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_12)); - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_12)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_12)); - __pyx_t_12 = 0; - __pyx_t_12 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_12); + PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_14); + __Pyx_GIVEREF(__pyx_t_14); + __pyx_t_14 = 0; + __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_14)); + __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0; + __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_13); + PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_14)); + __Pyx_GIVEREF(((PyObject *)__pyx_t_14)); + __pyx_t_14 = 0; + __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_14); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0; + __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; } @@ -11692,9 +11824,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_7); - __Pyx_XDECREF(__pyx_t_10); - __Pyx_XDECREF(__pyx_t_12); - __Pyx_AddTraceback("cvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_XDECREF(__pyx_t_13); + __Pyx_XDECREF(__pyx_t_14); + __Pyx_AddTraceback("pysam.cvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_key); @@ -11708,17 +11840,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_21parse_heading = {__Pyx_NAMESTR("parse_heading"), (PyCFunction)__pyx_pw_4cvcf_3VCF_21parse_heading, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_21parse_heading = {__Pyx_NAMESTR("parse_heading"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_line = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("parse_heading (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -11732,12 +11863,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -11758,16 +11887,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.parse_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_20parse_heading(__pyx_self, __pyx_v_self, __pyx_v_line); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(__pyx_self, __pyx_v_self, __pyx_v_line); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":553 +/* "pysam/cvcf.pyx":553 * * * def parse_heading( self, line ): # <<<<<<<<<<<<<< @@ -11775,7 +11904,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObj * assert not line.startswith('##') */ -static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line) { PyObject *__pyx_v_headings = NULL; PyObject *__pyx_v_i = NULL; PyObject *__pyx_v_s = NULL; @@ -11800,7 +11929,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p int __pyx_clineno = 0; __Pyx_RefNannySetupContext("parse_heading", 0); - /* "cvcf.pyx":554 + /* "pysam/cvcf.pyx":554 * * def parse_heading( self, line ): * assert line.startswith('#') # <<<<<<<<<<<<<< @@ -11821,7 +11950,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } #endif - /* "cvcf.pyx":555 + /* "pysam/cvcf.pyx":555 * def parse_heading( self, line ): * assert line.startswith('#') * assert not line.startswith('##') # <<<<<<<<<<<<<< @@ -11842,7 +11971,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } #endif - /* "cvcf.pyx":556 + /* "pysam/cvcf.pyx":556 * assert line.startswith('#') * assert not line.startswith('##') * headings = line[1:].split('\t') # <<<<<<<<<<<<<< @@ -11860,7 +11989,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __pyx_v_headings = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":558 + /* "pysam/cvcf.pyx":558 * headings = line[1:].split('\t') * # test for 8, as FORMAT field might be missing * if len(headings)==1 and len(line[1:].split()) >= 8: # <<<<<<<<<<<<<< @@ -11887,7 +12016,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } if (__pyx_t_6) { - /* "cvcf.pyx":559 + /* "pysam/cvcf.pyx":559 * # test for 8, as FORMAT field might be missing * if len(headings)==1 and len(line[1:].split()) >= 8: * self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS) # <<<<<<<<<<<<<< @@ -11912,7 +12041,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":560 + /* "pysam/cvcf.pyx":560 * if len(headings)==1 and len(line[1:].split()) >= 8: * self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS) * headings = line[1:].split() # <<<<<<<<<<<<<< @@ -11934,7 +12063,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } __pyx_L3:; - /* "cvcf.pyx":562 + /* "pysam/cvcf.pyx":562 * headings = line[1:].split() * * for i,s in enumerate(self._required): # <<<<<<<<<<<<<< @@ -11957,10 +12086,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p for (;;) { if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_7 = __pyx_t_8(__pyx_t_1); if (unlikely(!__pyx_t_7)) { @@ -11984,7 +12121,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __pyx_t_2 = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":564 + /* "pysam/cvcf.pyx":564 * for i,s in enumerate(self._required): * * if len(headings)<=i or headings[i] != s: # <<<<<<<<<<<<<< @@ -11994,16 +12131,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (!__pyx_t_6) { __pyx_t_10 = PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_7 = PyObject_RichCompare(__pyx_t_10, __pyx_v_s, Py_NE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_10, __pyx_v_s, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -12013,7 +12148,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } if (__pyx_t_5) { - /* "cvcf.pyx":566 + /* "pysam/cvcf.pyx":566 * if len(headings)<=i or headings[i] != s: * * if len(headings) <= i: # <<<<<<<<<<<<<< @@ -12023,14 +12158,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_5) { - /* "cvcf.pyx":567 + /* "pysam/cvcf.pyx":567 * * if len(headings) <= i: * err = "(%sth entry not found)" % (i+1) # <<<<<<<<<<<<<< @@ -12049,7 +12183,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } /*else*/ { - /* "cvcf.pyx":569 + /* "pysam/cvcf.pyx":569 * err = "(%sth entry not found)" % (i+1) * else: * err = "(found %s, expected %s)" % (headings[i],s) # <<<<<<<<<<<<<< @@ -12075,7 +12209,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } __pyx_L7:; - /* "cvcf.pyx":573 + /* "pysam/cvcf.pyx":573 * #self.error(line,self.BADLY_FORMATTED_HEADING,err) * # allow FORMAT column to be absent * if len(headings) == 8: # <<<<<<<<<<<<<< @@ -12086,7 +12220,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __pyx_t_5 = (__pyx_t_9 == 8); if (__pyx_t_5) { - /* "cvcf.pyx":574 + /* "pysam/cvcf.pyx":574 * # allow FORMAT column to be absent * if len(headings) == 8: * headings.append("FORMAT") # <<<<<<<<<<<<<< @@ -12100,7 +12234,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } /*else*/ { - /* "cvcf.pyx":576 + /* "pysam/cvcf.pyx":576 * headings.append("FORMAT") * else: * self.error(line,self.BADLY_FORMATTED_HEADING,err) # <<<<<<<<<<<<<< @@ -12136,7 +12270,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":578 + /* "pysam/cvcf.pyx":578 * self.error(line,self.BADLY_FORMATTED_HEADING,err) * * self._samples = headings[9:] # <<<<<<<<<<<<<< @@ -12148,7 +12282,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":579 + /* "pysam/cvcf.pyx":579 * * self._samples = headings[9:] * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) # <<<<<<<<<<<<<< @@ -12173,10 +12307,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p for (;;) { if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_11)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_11)) break; - __pyx_t_10 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_11)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_11)) break; - __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_10 = __pyx_t_8(__pyx_t_11); if (unlikely(!__pyx_t_10)) { @@ -12209,7 +12351,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_10); __Pyx_GIVEREF(__pyx_t_10); __pyx_t_10 = 0; - if (unlikely(PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; } __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; @@ -12234,7 +12376,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p __Pyx_XDECREF(__pyx_t_7); __Pyx_XDECREF(__pyx_t_10); __Pyx_XDECREF(__pyx_t_11); - __Pyx_AddTraceback("cvcf.VCF.parse_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_headings); @@ -12249,17 +12391,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__p } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_23write_heading = {__Pyx_NAMESTR("write_heading"), (PyCFunction)__pyx_pw_4cvcf_3VCF_23write_heading, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_23write_heading = {__Pyx_NAMESTR("write_heading"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_23write_heading, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("write_heading (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -12273,12 +12414,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -12299,16 +12438,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.write_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.write_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_22write_heading(__pyx_self, __pyx_v_self, __pyx_v_stream); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_22write_heading(__pyx_self, __pyx_v_self, __pyx_v_stream); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":581 +/* "pysam/cvcf.pyx":581 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) * * def write_heading( self, stream ): # <<<<<<<<<<<<<< @@ -12316,7 +12455,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObj * */ -static PyObject *__pyx_pf_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -12329,7 +12468,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__p int __pyx_clineno = 0; __Pyx_RefNannySetupContext("write_heading", 0); - /* "cvcf.pyx":582 + /* "pysam/cvcf.pyx":582 * * def write_heading( self, stream ): * stream.write("#" + "\t".join(self._required + self._samples) + "\n") # <<<<<<<<<<<<<< @@ -12382,7 +12521,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__p __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); - __Pyx_AddTraceback("cvcf.VCF.write_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.write_heading", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -12391,17 +12530,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__p } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_25convertGT = {__Pyx_NAMESTR("convertGT"), (PyCFunction)__pyx_pw_4cvcf_3VCF_25convertGT, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_25convertGT = {__Pyx_NAMESTR("convertGT"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_25convertGT, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_GTstring = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTstring,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("convertGT (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTstring,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -12415,12 +12553,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTstring); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTstring)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -12441,16 +12577,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_24convertGT(__pyx_self, __pyx_v_self, __pyx_v_GTstring); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_24convertGT(__pyx_self, __pyx_v_self, __pyx_v_GTstring); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":584 +/* "pysam/cvcf.pyx":584 * stream.write("#" + "\t".join(self._required + self._samples) + "\n") * * def convertGT(self, GTstring): # <<<<<<<<<<<<<< @@ -12458,12 +12594,12 @@ static PyObject *__pyx_pw_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject * try: */ -static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring) { PyObject *__pyx_v_gts = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - int __pyx_t_1; - PyObject *__pyx_t_2 = NULL; + PyObject *__pyx_t_1 = NULL; + int __pyx_t_2; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; @@ -12483,29 +12619,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("convertGT", 0); - /* "cvcf.pyx":585 + /* "pysam/cvcf.pyx":585 * * def convertGT(self, GTstring): * if GTstring == ".": return ["."] # <<<<<<<<<<<<<< * try: * gts = gtsRegEx.split(GTstring) */ - __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__pyx_t_1) { + __pyx_t_1 = PyObject_RichCompare(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + if (__pyx_t_2) { __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_kp_s_9)); - PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_9)); + PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_9)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); - __pyx_r = ((PyObject *)__pyx_t_2); - __pyx_t_2 = 0; + __pyx_r = ((PyObject *)__pyx_t_1); + __pyx_t_1 = 0; goto __pyx_L0; goto __pyx_L3; } __pyx_L3:; - /* "cvcf.pyx":586 + /* "pysam/cvcf.pyx":586 * def convertGT(self, GTstring): * if GTstring == ".": return ["."] * try: # <<<<<<<<<<<<<< @@ -12519,31 +12657,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s __Pyx_XGOTREF(__pyx_t_5); /*try:*/ { - /* "cvcf.pyx":587 + /* "pysam/cvcf.pyx":587 * if GTstring == ".": return ["."] * try: * gts = gtsRegEx.split(GTstring) # <<<<<<<<<<<<<< * if len(gts) == 1: return [int(gts[0])] * if len(gts) != 2: raise ValueError() */ - __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__gtsRegEx); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_6 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__gtsRegEx); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_6); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_GTstring); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_GTstring); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_GTstring); __Pyx_GIVEREF(__pyx_v_GTstring); - __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_v_gts = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":588 + /* "pysam/cvcf.pyx":588 * try: * gts = gtsRegEx.split(GTstring) * if len(gts) == 1: return [int(gts[0])] # <<<<<<<<<<<<<< @@ -12551,32 +12689,32 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] */ __pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __pyx_t_1 = (__pyx_t_8 == 1); - if (__pyx_t_1) { + __pyx_t_2 = (__pyx_t_8 == 1); + if (__pyx_t_2) { __Pyx_XDECREF(__pyx_r); __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7); + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_7); + __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); + PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_r = ((PyObject *)__pyx_t_2); - __pyx_t_2 = 0; + __pyx_r = ((PyObject *)__pyx_t_1); + __pyx_t_1 = 0; goto __pyx_L8_try_return; goto __pyx_L12; } __pyx_L12:; - /* "cvcf.pyx":589 + /* "pysam/cvcf.pyx":589 * gts = gtsRegEx.split(GTstring) * if len(gts) == 1: return [int(gts[0])] * if len(gts) != 2: raise ValueError() # <<<<<<<<<<<<<< @@ -12584,41 +12722,45 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] */ __pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __pyx_t_1 = (__pyx_t_8 != 2); - if (__pyx_t_1) { - __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_Raise(__pyx_t_2, 0, 0, 0); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = (__pyx_t_8 != 2); + if (__pyx_t_2) { + __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_Raise(__pyx_t_1, 0, 0, 0); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;} goto __pyx_L13; } __pyx_L13:; - /* "cvcf.pyx":590 + /* "pysam/cvcf.pyx":590 * if len(gts) == 1: return [int(gts[0])] * if len(gts) != 2: raise ValueError() * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] # <<<<<<<<<<<<<< * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] * except ValueError: */ - __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (__pyx_t_1) { - __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + if (__pyx_t_2) { + __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_7); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; + __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_10 = __pyx_t_9; } else { - __pyx_t_10 = __pyx_t_1; + __pyx_t_10 = __pyx_t_2; } if (__pyx_t_10) { __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_8 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} @@ -12633,13 +12775,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s __Pyx_GOTREF(__pyx_t_6); __pyx_t_12 = PyList_New(3); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_12); - PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); + PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_1); + __Pyx_GIVEREF(__pyx_t_1); PyList_SET_ITEM(__pyx_t_12, 1, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); PyList_SET_ITEM(__pyx_t_12, 2, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); - __pyx_t_2 = 0; + __pyx_t_1 = 0; __pyx_t_7 = 0; __pyx_t_6 = 0; __pyx_r = ((PyObject *)__pyx_t_12); @@ -12649,7 +12791,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s } __pyx_L14:; - /* "cvcf.pyx":591 + /* "pysam/cvcf.pyx":591 * if len(gts) != 2: raise ValueError() * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] # <<<<<<<<<<<<<< @@ -12679,27 +12821,27 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7); + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_2 = PyList_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_2); - PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_12); + __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + __pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __Pyx_GOTREF(__pyx_t_1); + PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_12); __Pyx_GIVEREF(__pyx_t_12); - PyList_SET_ITEM(__pyx_t_2, 1, __pyx_t_6); + PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); - PyList_SET_ITEM(__pyx_t_2, 2, __pyx_t_7); + PyList_SET_ITEM(__pyx_t_1, 2, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_12 = 0; __pyx_t_6 = 0; __pyx_t_7 = 0; - __pyx_r = ((PyObject *)__pyx_t_2); - __pyx_t_2 = 0; + __pyx_r = ((PyObject *)__pyx_t_1); + __pyx_t_1 = 0; goto __pyx_L8_try_return; } __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -12716,9 +12858,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0; __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; - __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":592 + /* "pysam/cvcf.pyx":592 * if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] * except ValueError: # <<<<<<<<<<<<<< @@ -12727,13 +12869,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_t_13 = PyErr_ExceptionMatches(__pyx_builtin_ValueError); if (__pyx_t_13) { - __Pyx_AddTraceback("cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_AddTraceback("pysam.cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_GOTREF(__pyx_t_7); __Pyx_GOTREF(__pyx_t_6); - /* "cvcf.pyx":593 + /* "pysam/cvcf.pyx":593 * return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] * except ValueError: * self.error(self._line,self.BAD_GENOTYPE,GTstring) # <<<<<<<<<<<<<< @@ -12763,7 +12905,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s __Pyx_DECREF(((PyObject *)__pyx_t_16)); __pyx_t_16 = 0; __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; - /* "cvcf.pyx":594 + /* "pysam/cvcf.pyx":594 * except ValueError: * self.error(self._line,self.BAD_GENOTYPE,GTstring) * return [".","|","."] # <<<<<<<<<<<<<< @@ -12784,11 +12926,11 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); __pyx_r = ((PyObject *)__pyx_t_15); __pyx_t_15 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; goto __pyx_L7_except_return; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; goto __pyx_L5_exception_handled; @@ -12816,14 +12958,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_7); __Pyx_XDECREF(__pyx_t_12); __Pyx_XDECREF(__pyx_t_14); __Pyx_XDECREF(__pyx_t_15); __Pyx_XDECREF(__pyx_t_16); - __Pyx_AddTraceback("cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_gts); @@ -12833,17 +12975,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_27convertGTback = {__Pyx_NAMESTR("convertGTback"), (PyCFunction)__pyx_pw_4cvcf_3VCF_27convertGTback, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_27convertGTback = {__Pyx_NAMESTR("convertGTback"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { CYTHON_UNUSED PyObject *__pyx_v_self = 0; PyObject *__pyx_v_GTdata = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTdata,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("convertGTback (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTdata,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -12857,12 +12998,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTdata); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTdata)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -12883,16 +13022,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.convertGTback", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.convertGTback", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_26convertGTback(__pyx_self, __pyx_v_self, __pyx_v_GTdata); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(__pyx_self, __pyx_v_self, __pyx_v_GTdata); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":596 +/* "pysam/cvcf.pyx":596 * return [".","|","."] * * def convertGTback(self, GTdata): # <<<<<<<<<<<<<< @@ -12900,7 +13039,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObj * */ -static PyObject *__pyx_pf_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -12911,7 +13050,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__p int __pyx_clineno = 0; __Pyx_RefNannySetupContext("convertGTback", 0); - /* "cvcf.pyx":597 + /* "pysam/cvcf.pyx":597 * * def convertGTback(self, GTdata): * return ''.join(map(str,GTdata)) # <<<<<<<<<<<<<< @@ -12951,7 +13090,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__p __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("cvcf.VCF.convertGTback", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.convertGTback", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -12960,20 +13099,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__p } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_29parse_formatdata = {__Pyx_NAMESTR("parse_formatdata"), (PyCFunction)__pyx_pw_4cvcf_3VCF_29parse_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_29parse_formatdata = {__Pyx_NAMESTR("parse_formatdata"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_29parse_formatdata, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_key = 0; PyObject *__pyx_v_value = 0; PyObject *__pyx_v_formatdict = 0; PyObject *__pyx_v_line = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__formatdict,&__pyx_n_s__line,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("parse_formatdata (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__formatdict,&__pyx_n_s__line,0}; PyObject* values[5] = {0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -12990,30 +13128,25 @@ static PyObject *__pyx_pw_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_self, Py kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict); - if (likely(values[3])) kw_args--; + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: - values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[4])) kw_args--; + if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -13040,16 +13173,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_self, Py __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_28parse_formatdata(__pyx_self, __pyx_v_self, __pyx_v_key, __pyx_v_value, __pyx_v_formatdict, __pyx_v_line); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(__pyx_self, __pyx_v_self, __pyx_v_key, __pyx_v_value, __pyx_v_formatdict, __pyx_v_line); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":599 +/* "pysam/cvcf.pyx":599 * return ''.join(map(str,GTdata)) * * def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<< @@ -13057,7 +13190,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_self, Py * f = formatdict.get(key,None) */ -static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line) { PyObject *__pyx_v_f = NULL; PyObject *__pyx_v_values = NULL; PyObject *__pyx_v_idx = NULL; @@ -13088,7 +13221,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * int __pyx_clineno = 0; __Pyx_RefNannySetupContext("parse_formatdata", 0); - /* "cvcf.pyx":601 + /* "pysam/cvcf.pyx":601 * def parse_formatdata( self, key, value, formatdict, line ): * # To do: check that the right number of values is present * f = formatdict.get(key,None) # <<<<<<<<<<<<<< @@ -13112,20 +13245,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __pyx_v_f = __pyx_t_3; __pyx_t_3 = 0; - /* "cvcf.pyx":602 + /* "pysam/cvcf.pyx":602 * # To do: check that the right number of values is present * f = formatdict.get(key,None) * if f == None: # <<<<<<<<<<<<<< * self._add_definition(formatdict, key, value, line ) * f = formatdict[key] */ - __pyx_t_3 = PyObject_RichCompare(__pyx_v_f, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_f, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_4) { - /* "cvcf.pyx":603 + /* "pysam/cvcf.pyx":603 * f = formatdict.get(key,None) * if f == None: * self._add_definition(formatdict, key, value, line ) # <<<<<<<<<<<<<< @@ -13154,7 +13286,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":604 + /* "pysam/cvcf.pyx":604 * if f == None: * self._add_definition(formatdict, key, value, line ) * f = formatdict[key] # <<<<<<<<<<<<<< @@ -13170,7 +13302,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * } __pyx_L3:; - /* "cvcf.pyx":605 + /* "pysam/cvcf.pyx":605 * self._add_definition(formatdict, key, value, line ) * f = formatdict[key] * if f.type == "Flag": # <<<<<<<<<<<<<< @@ -13179,11 +13311,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_4) { - /* "cvcf.pyx":606 + /* "pysam/cvcf.pyx":606 * f = formatdict[key] * if f.type == "Flag": * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) # <<<<<<<<<<<<<< @@ -13192,28 +13326,28 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * */ __pyx_t_4 = (__pyx_v_value != Py_None); if (__pyx_t_4) { - __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_96); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_96); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); - __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1); + __Pyx_GIVEREF(__pyx_t_1); + __pyx_t_1 = 0; + __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L5; } __pyx_L5:; - /* "cvcf.pyx":607 + /* "pysam/cvcf.pyx":607 * if f.type == "Flag": * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) * return [] # <<<<<<<<<<<<<< @@ -13221,31 +13355,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * * # deal with trailing data in some early VCF files */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_r = ((PyObject *)__pyx_t_2); - __pyx_t_2 = 0; + __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_r = ((PyObject *)__pyx_t_1); + __pyx_t_1 = 0; goto __pyx_L0; goto __pyx_L4; } __pyx_L4:; - /* "cvcf.pyx":608 + /* "pysam/cvcf.pyx":608 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) * return [] * values = value.split(',') # <<<<<<<<<<<<<< * # deal with trailing data in some early VCF files * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_v_values = __pyx_t_3; __pyx_t_3 = 0; - /* "cvcf.pyx":610 + /* "pysam/cvcf.pyx":610 * values = value.split(',') * # deal with trailing data in some early VCF files * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: # <<<<<<<<<<<<<< @@ -13254,9 +13388,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * */ __pyx_t_3 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_3, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (!((int)__pyx_t_4)) { - __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_3, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_6 = ((int)__pyx_t_5); } else { __pyx_t_6 = ((int)__pyx_t_4); @@ -13269,17 +13407,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * if (__pyx_t_6) { __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__find); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__find); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_int_neg_1, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_int_neg_1, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_8 = __pyx_t_5; } else { __pyx_t_8 = __pyx_t_6; @@ -13290,19 +13427,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * } if (__pyx_t_6) { - /* "cvcf.pyx":611 + /* "pysam/cvcf.pyx":611 * # deal with trailing data in some early VCF files * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: * self.error(line,self.ERROR_TRAILING_DATA,values[-1]) # <<<<<<<<<<<<<< * values[-1] = values[-1].split(';')[0] * if f.type == "Integer": */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_TRAILING_DATA); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_INCREF(__pyx_v_line); @@ -13310,41 +13447,41 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_GIVEREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_1); - __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); __pyx_t_3 = 0; - __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":612 + /* "pysam/cvcf.pyx":612 * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: * self.error(line,self.ERROR_TRAILING_DATA,values[-1]) * values[-1] = values[-1].split(';')[0] # <<<<<<<<<<<<<< * if f.type == "Integer": * for idx,v in enumerate(values): */ - __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_9 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_1, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_2, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__Pyx_SetItemInt(__pyx_v_values, -1, __pyx_t_9, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L6; } __pyx_L6:; - /* "cvcf.pyx":613 + /* "pysam/cvcf.pyx":613 * self.error(line,self.ERROR_TRAILING_DATA,values[-1]) * values[-1] = values[-1].split(';')[0] * if f.type == "Integer": # <<<<<<<<<<<<<< @@ -13353,11 +13490,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * */ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_6) { - /* "cvcf.pyx":614 + /* "pysam/cvcf.pyx":614 * values[-1] = values[-1].split(';')[0] * if f.type == "Integer": * for idx,v in enumerate(values): # <<<<<<<<<<<<<< @@ -13365,46 +13504,54 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * * if v == ".": values[idx] = f.missingvalue */ __Pyx_INCREF(__pyx_int_0); - __pyx_t_9 = __pyx_int_0; + __pyx_t_2 = __pyx_int_0; if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) { - __pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1); __pyx_t_7 = 0; + __pyx_t_9 = __pyx_v_values; __Pyx_INCREF(__pyx_t_9); __pyx_t_7 = 0; __pyx_t_10 = NULL; } else { - __pyx_t_7 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_10 = Py_TYPE(__pyx_t_1)->tp_iternext; + __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext; } for (;;) { - if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) { - if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; - } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) { - if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; + if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) { + if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) { + if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_2 = __pyx_t_10(__pyx_t_1); - if (unlikely(!__pyx_t_2)) { + __pyx_t_1 = __pyx_t_10(__pyx_t_9); + if (unlikely(!__pyx_t_1)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_1); } __Pyx_XDECREF(__pyx_v_v); - __pyx_v_v = __pyx_t_2; - __pyx_t_2 = 0; - __Pyx_INCREF(__pyx_t_9); + __pyx_v_v = __pyx_t_1; + __pyx_t_1 = 0; + __Pyx_INCREF(__pyx_t_2); __Pyx_XDECREF(__pyx_v_idx); - __pyx_v_idx = __pyx_t_9; - __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_9); - __pyx_t_9 = __pyx_t_2; - __pyx_t_2 = 0; + __pyx_v_idx = __pyx_t_2; + __pyx_t_1 = PyNumber_Add(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_2); + __pyx_t_2 = __pyx_t_1; + __pyx_t_1 = 0; - /* "cvcf.pyx":615 + /* "pysam/cvcf.pyx":615 * if f.type == "Integer": * for idx,v in enumerate(values): * try: # <<<<<<<<<<<<<< @@ -13418,38 +13565,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_XGOTREF(__pyx_t_13); /*try:*/ { - /* "cvcf.pyx":616 + /* "pysam/cvcf.pyx":616 * for idx,v in enumerate(values): * try: * if v == ".": values[idx] = f.missingvalue # <<<<<<<<<<<<<< * else: values[idx] = int(v) * except: */ - __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_6) { - __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;} - __Pyx_GOTREF(__pyx_t_2); - if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L18; } /*else*/ { - /* "cvcf.pyx":617 + /* "pysam/cvcf.pyx":617 * try: * if v == ".": values[idx] = f.missingvalue * else: values[idx] = int(v) # <<<<<<<<<<<<<< * except: * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) */ - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_v); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_v); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_v); __Pyx_GIVEREF(__pyx_v_v); - __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;} __Pyx_GOTREF(__pyx_t_3); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; } @@ -13460,10 +13609,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0; goto __pyx_L17_try_end; __pyx_L10_error:; - __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":618 + /* "pysam/cvcf.pyx":618 * if v == ".": values[idx] = f.missingvalue * else: values[idx] = int(v) * except: # <<<<<<<<<<<<<< @@ -13471,13 +13620,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * * return [0] * len(values) */ /*except:*/ { - __Pyx_AddTraceback("cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_2, &__pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;} + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_1, &__pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;} __Pyx_GOTREF(__pyx_t_3); - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_1); __Pyx_GOTREF(__pyx_t_14); - /* "cvcf.pyx":619 + /* "pysam/cvcf.pyx":619 * else: values[idx] = int(v) * except: * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) # <<<<<<<<<<<<<< @@ -13524,7 +13673,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_DECREF(((PyObject *)__pyx_t_17)); __pyx_t_17 = 0; __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; - /* "cvcf.pyx":620 + /* "pysam/cvcf.pyx":620 * except: * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) * return [0] * len(values) # <<<<<<<<<<<<<< @@ -13551,7 +13700,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; goto __pyx_L13_except_return; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; goto __pyx_L11_exception_handled; } @@ -13575,10 +13724,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __pyx_L17_try_end:; } } - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":621 + /* "pysam/cvcf.pyx":621 * self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) * return [0] * len(values) * return values # <<<<<<<<<<<<<< @@ -13592,20 +13741,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * goto __pyx_L7; } - /* "cvcf.pyx":622 + /* "pysam/cvcf.pyx":622 * return [0] * len(values) * return values * elif f.type == "String": # <<<<<<<<<<<<<< * self._line = line * if f.id == "GT": values = list(map( self.convertGT, values )) */ - __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__String), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__String), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_6) { - /* "cvcf.pyx":623 + /* "pysam/cvcf.pyx":623 * return values * elif f.type == "String": * self._line = line # <<<<<<<<<<<<<< @@ -13614,7 +13765,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * */ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___line, __pyx_v_line) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 623; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":624 + /* "pysam/cvcf.pyx":624 * elif f.type == "String": * self._line = line * if f.id == "GT": values = list(map( self.convertGT, values )) # <<<<<<<<<<<<<< @@ -13623,38 +13774,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * */ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__GT), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__GT), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_6) { - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGT); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_values); - PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_values); + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_values); __Pyx_GIVEREF(__pyx_v_values); - __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); - __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_v_values); - __pyx_v_values = __pyx_t_9; - __pyx_t_9 = 0; + __pyx_v_values = __pyx_t_2; + __pyx_t_2 = 0; goto __pyx_L21; } __pyx_L21:; - /* "cvcf.pyx":625 + /* "pysam/cvcf.pyx":625 * self._line = line * if f.id == "GT": values = list(map( self.convertGT, values )) * return values # <<<<<<<<<<<<<< @@ -13668,20 +13821,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * goto __pyx_L7; } - /* "cvcf.pyx":626 + /* "pysam/cvcf.pyx":626 * if f.id == "GT": values = list(map( self.convertGT, values )) * return values * elif f.type == "Character": # <<<<<<<<<<<<<< * for v in values: * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) */ - __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Character), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__Character), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_6) { - /* "cvcf.pyx":627 + /* "pysam/cvcf.pyx":627 * return values * elif f.type == "Character": * for v in values: # <<<<<<<<<<<<<< @@ -13699,26 +13854,34 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * for (;;) { if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) { if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break; - __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) { if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break; - __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_1 = __pyx_t_10(__pyx_t_9); - if (unlikely(!__pyx_t_1)) { + __pyx_t_2 = __pyx_t_10(__pyx_t_9); + if (unlikely(!__pyx_t_2)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(__pyx_t_2); } __Pyx_XDECREF(__pyx_v_v); - __pyx_v_v = __pyx_t_1; - __pyx_t_1 = 0; + __pyx_v_v = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":628 + /* "pysam/cvcf.pyx":628 * elif f.type == "Character": * for v in values: * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) # <<<<<<<<<<<<<< @@ -13728,22 +13891,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __pyx_t_19 = PyObject_Length(__pyx_v_v); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = (__pyx_t_19 != 1); if (__pyx_t_6) { - __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_101); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_14); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_14); + PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_14); __Pyx_GIVEREF(__pyx_t_14); __pyx_t_14 = 0; - __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_14); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; goto __pyx_L24; } @@ -13751,7 +13914,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * } __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "cvcf.pyx":629 + /* "pysam/cvcf.pyx":629 * for v in values: * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) * return values # <<<<<<<<<<<<<< @@ -13765,7 +13928,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * goto __pyx_L7; } - /* "cvcf.pyx":630 + /* "pysam/cvcf.pyx":630 * if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) * return values * elif f.type == "Float": # <<<<<<<<<<<<<< @@ -13774,11 +13937,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * */ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; if (__pyx_t_6) { - /* "cvcf.pyx":631 + /* "pysam/cvcf.pyx":631 * return values * elif f.type == "Float": * for idx,v in enumerate(values): # <<<<<<<<<<<<<< @@ -13786,66 +13951,76 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * * try: return list(map(float,values)) */ __Pyx_INCREF(__pyx_int_0); - __pyx_t_9 = __pyx_int_0; + __pyx_t_14 = __pyx_int_0; if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) { - __pyx_t_14 = __pyx_v_values; __Pyx_INCREF(__pyx_t_14); __pyx_t_7 = 0; + __pyx_t_9 = __pyx_v_values; __Pyx_INCREF(__pyx_t_9); __pyx_t_7 = 0; __pyx_t_10 = NULL; } else { - __pyx_t_7 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); - __pyx_t_10 = Py_TYPE(__pyx_t_14)->tp_iternext; + __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext; } for (;;) { - if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_14)) { - if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_14)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; - } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_14)) { - if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_14)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; + if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) { + if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) { + if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_2 = __pyx_t_10(__pyx_t_14); - if (unlikely(!__pyx_t_2)) { + __pyx_t_1 = __pyx_t_10(__pyx_t_9); + if (unlikely(!__pyx_t_1)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_1); } __Pyx_XDECREF(__pyx_v_v); - __pyx_v_v = __pyx_t_2; - __pyx_t_2 = 0; - __Pyx_INCREF(__pyx_t_9); + __pyx_v_v = __pyx_t_1; + __pyx_t_1 = 0; + __Pyx_INCREF(__pyx_t_14); __Pyx_XDECREF(__pyx_v_idx); - __pyx_v_idx = __pyx_t_9; - __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_9); - __pyx_t_9 = __pyx_t_2; - __pyx_t_2 = 0; + __pyx_v_idx = __pyx_t_14; + __pyx_t_1 = PyNumber_Add(__pyx_t_14, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_14); + __pyx_t_14 = __pyx_t_1; + __pyx_t_1 = 0; - /* "cvcf.pyx":632 + /* "pysam/cvcf.pyx":632 * elif f.type == "Float": * for idx,v in enumerate(values): * if v == ".": values[idx] = f.missingvalue # <<<<<<<<<<<<<< * try: return list(map(float,values)) * except: */ - __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_6) { - __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L27; } __pyx_L27:; } - __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - /* "cvcf.pyx":633 + /* "pysam/cvcf.pyx":633 * for idx,v in enumerate(values): * if v == ".": values[idx] = f.missingvalue * try: return list(map(float,values)) # <<<<<<<<<<<<<< @@ -13859,27 +14034,27 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_XGOTREF(__pyx_t_11); /*try:*/ { __Pyx_XDECREF(__pyx_r); - __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_14 = PyTuple_New(2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} + __Pyx_GOTREF(__pyx_t_14); __Pyx_INCREF(((PyObject *)((PyObject*)(&PyFloat_Type)))); - PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)(&PyFloat_Type)))); + PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)((PyObject*)(&PyFloat_Type)))); __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyFloat_Type)))); __Pyx_INCREF(__pyx_v_values); - PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_values); + PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_v_values); __Pyx_GIVEREF(__pyx_v_values); - __pyx_t_14 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} - __Pyx_GOTREF(__pyx_t_14); - __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; - __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} + __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} __Pyx_GOTREF(__pyx_t_9); - PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_14); - __Pyx_GIVEREF(__pyx_t_14); - __pyx_t_14 = 0; - __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} + __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0; + __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} __Pyx_GOTREF(__pyx_t_14); - __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; - __pyx_r = __pyx_t_14; - __pyx_t_14 = 0; + PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_9); + __Pyx_GIVEREF(__pyx_t_9); + __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0; + __pyx_r = __pyx_t_9; + __pyx_t_9 = 0; goto __pyx_L32_try_return; } __Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0; @@ -13898,12 +14073,12 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0; __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0; + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "cvcf.pyx":634 + /* "pysam/cvcf.pyx":634 * if v == ".": values[idx] = f.missingvalue * try: return list(map(float,values)) * except: # <<<<<<<<<<<<<< @@ -13911,21 +14086,21 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * * return [0.0] * len(values) */ /*except:*/ { - __Pyx_AddTraceback("cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_14, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} - __Pyx_GOTREF(__pyx_t_14); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_14, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_14); + __Pyx_GOTREF(__pyx_t_1); - /* "cvcf.pyx":635 + /* "pysam/cvcf.pyx":635 * try: return list(map(float,values)) * except: * self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values))) # <<<<<<<<<<<<<< * return [0.0] * len(values) * else: */ - __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} + __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} @@ -13958,13 +14133,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_GIVEREF(((PyObject *)__pyx_t_17)); __pyx_t_3 = 0; __pyx_t_17 = 0; - __pyx_t_17 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} + __pyx_t_17 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} __Pyx_GOTREF(__pyx_t_17); - __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_18)); __pyx_t_18 = 0; __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; - /* "cvcf.pyx":636 + /* "pysam/cvcf.pyx":636 * except: * self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values))) * return [0.0] * len(values) # <<<<<<<<<<<<<< @@ -13987,13 +14162,13 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0; __pyx_r = ((PyObject *)__pyx_t_18); __pyx_t_18 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; goto __pyx_L31_except_return; - __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L29_exception_handled; } __pyx_L30_except_error:; @@ -14019,30 +14194,30 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * } /*else*/ { - /* "cvcf.pyx":639 + /* "pysam/cvcf.pyx":639 * else: * # can't happen * self.error(line,self.ERROR_INFO_STRING) # <<<<<<<<<<<<<< * * def inregion(self, chrom, pos): */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_14 = PyTuple_New(2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_14); + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); - __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0; - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_14); + __Pyx_GIVEREF(__pyx_t_14); + __pyx_t_14 = 0; + __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_14); + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; } __pyx_L7:; @@ -14058,7 +14233,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * __Pyx_XDECREF(__pyx_t_16); __Pyx_XDECREF(__pyx_t_17); __Pyx_XDECREF(__pyx_t_18); - __Pyx_AddTraceback("cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_f); @@ -14071,18 +14246,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject * } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_31inregion = {__Pyx_NAMESTR("inregion"), (PyCFunction)__pyx_pw_4cvcf_3VCF_31inregion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_31inregion = {__Pyx_NAMESTR("inregion"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_31inregion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_chrom = 0; PyObject *__pyx_v_pos = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__chrom,&__pyx_n_s__pos,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("inregion (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__chrom,&__pyx_n_s__pos,0}; PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -14097,18 +14271,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyObject * kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -14131,16 +14302,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyObject * __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.inregion", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.inregion", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_30inregion(__pyx_self, __pyx_v_self, __pyx_v_chrom, __pyx_v_pos); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_30inregion(__pyx_self, __pyx_v_self, __pyx_v_chrom, __pyx_v_pos); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":641 +/* "pysam/cvcf.pyx":641 * self.error(line,self.ERROR_INFO_STRING) * * def inregion(self, chrom, pos): # <<<<<<<<<<<<<< @@ -14148,7 +14319,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyObject * * for r in self._regions: */ -static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos) { PyObject *__pyx_v_r = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -14166,7 +14337,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se int __pyx_clineno = 0; __Pyx_RefNannySetupContext("inregion", 0); - /* "cvcf.pyx":642 + /* "pysam/cvcf.pyx":642 * * def inregion(self, chrom, pos): * if not self._regions: return True # <<<<<<<<<<<<<< @@ -14189,7 +14360,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se } __pyx_L3:; - /* "cvcf.pyx":643 + /* "pysam/cvcf.pyx":643 * def inregion(self, chrom, pos): * if not self._regions: return True * for r in self._regions: # <<<<<<<<<<<<<< @@ -14210,10 +14381,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se for (;;) { if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break; - __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) { if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break; - __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_1 = __pyx_t_6(__pyx_t_4); if (unlikely(!__pyx_t_1)) { @@ -14229,7 +14408,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se __pyx_v_r = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":644 + /* "pysam/cvcf.pyx":644 * if not self._regions: return True * for r in self._regions: * if r[0] == chrom and r[1] <= pos < r[2]: return True # <<<<<<<<<<<<<< @@ -14238,22 +14417,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se */ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_r, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_v_chrom, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_v_chrom, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; if (__pyx_t_3) { __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_r, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, __pyx_v_pos, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, __pyx_v_pos, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_PyObject_IsTrue(__pyx_t_1)) { __Pyx_DECREF(__pyx_t_1); __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_r, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos, __pyx_t_8, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos, __pyx_t_8, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; } __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -14277,7 +14453,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":645 + /* "pysam/cvcf.pyx":645 * for r in self._regions: * if r[0] == chrom and r[1] <= pos < r[2]: return True * return False # <<<<<<<<<<<<<< @@ -14298,7 +14474,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_7); __Pyx_XDECREF(__pyx_t_8); - __Pyx_AddTraceback("cvcf.VCF.inregion", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.inregion", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_r); @@ -14307,7 +14483,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se return __pyx_r; } -/* "cvcf.pyx":647 +/* "pysam/cvcf.pyx":647 * return False * * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< @@ -14315,7 +14491,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_se * if len(cols) != len(self._samples)+9: */ -static PyObject *__pyx_pf_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -14337,7 +14513,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__py goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.__defaults__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -14346,18 +14522,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_33parse_data = {__Pyx_NAMESTR("parse_data"), (PyCFunction)__pyx_pw_4cvcf_3VCF_33parse_data, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_33parse_data = {__Pyx_NAMESTR("parse_data"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_33parse_data, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_line = 0; PyObject *__pyx_v_lineparse = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__lineparse,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("parse_data (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__lineparse,0}; PyObject* values[3] = {0,0,0}; __pyx_defaults4 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults4, __pyx_self); values[2] = __pyx_dynamic_args->__pyx_arg_lineparse; @@ -14374,12 +14549,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -14409,17 +14582,17 @@ static PyObject *__pyx_pw_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_32parse_data(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_lineparse); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_32parse_data(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_lineparse); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_gb_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ +static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ -/* "cvcf.pyx":790 +/* "pysam/cvcf.pyx":790 * if alt: * for i in range(1,min(len(ref),min(map(len,alt)))): * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<< @@ -14427,25 +14600,25 @@ static PyObject *__pyx_gb_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObj * ref, alt = ref[:-1], [allele[:-1] for allele in alt] */ -static PyObject *__pyx_pf_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self) { - struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *__pyx_cur_scope; +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *__pyx_cur_scope; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("genexpr", 0); - __pyx_cur_scope = (struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)__pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL); + __pyx_cur_scope = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL); if (unlikely(!__pyx_cur_scope)) { __Pyx_RefNannyFinishContext(); return NULL; } __Pyx_GOTREF(__pyx_cur_scope); - __pyx_cur_scope->__pyx_outer_scope = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *) __pyx_self; + __pyx_cur_scope->__pyx_outer_scope = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *) __pyx_self; __Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope)); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope); { - __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_4cvcf_3VCF_10parse_data_2generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_cur_scope); __Pyx_RefNannyFinishContext(); return (PyObject *) gen; @@ -14454,7 +14627,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self) __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.parse_data.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_data.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_DECREF(((PyObject *)__pyx_cur_scope)); @@ -14463,9 +14636,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self) return __pyx_r; } -static PyObject *__pyx_gb_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */ +static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */ { - struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *__pyx_cur_scope = ((struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)__pyx_generator->closure); + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *__pyx_cur_scope = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)__pyx_generator->closure); PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; Py_ssize_t __pyx_t_2; @@ -14495,10 +14668,18 @@ static PyObject *__pyx_gb_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObj for (;;) { if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_4 = __pyx_t_3(__pyx_t_1); if (unlikely(!__pyx_t_4)) { @@ -14553,11 +14734,12 @@ static PyObject *__pyx_gb_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObj __pyx_L0:; __Pyx_XDECREF(__pyx_r); __pyx_generator->resume_label = -1; + __Pyx_Generator_clear((PyObject*)__pyx_generator); __Pyx_RefNannyFinishContext(); return NULL; } -/* "cvcf.pyx":647 +/* "pysam/cvcf.pyx":647 * return False * * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< @@ -14565,8 +14747,8 @@ static PyObject *__pyx_gb_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObj * if len(cols) != len(self._samples)+9: */ -static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse) { - struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *__pyx_cur_scope; +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *__pyx_cur_scope; PyObject *__pyx_v_cols = NULL; PyObject *__pyx_v_chrom = NULL; PyObject *__pyx_v_pos = NULL; @@ -14639,14 +14821,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("parse_data", 0); - __pyx_cur_scope = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)__pyx_ptype_4cvcf___pyx_scope_struct__parse_data->tp_new(__pyx_ptype_4cvcf___pyx_scope_struct__parse_data, __pyx_empty_tuple, NULL); + __pyx_cur_scope = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)__pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data->tp_new(__pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data, __pyx_empty_tuple, NULL); if (unlikely(!__pyx_cur_scope)) { __Pyx_RefNannyFinishContext(); return NULL; } __Pyx_GOTREF(__pyx_cur_scope); - /* "cvcf.pyx":648 + /* "pysam/cvcf.pyx":648 * * def parse_data( self, line, lineparse=False ): * cols = line.split('\t') # <<<<<<<<<<<<<< @@ -14661,7 +14843,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_cols = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":649 + /* "pysam/cvcf.pyx":649 * def parse_data( self, line, lineparse=False ): * cols = line.split('\t') * if len(cols) != len(self._samples)+9: # <<<<<<<<<<<<<< @@ -14676,7 +14858,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_5 = (__pyx_t_3 != (__pyx_t_4 + 9)); if (__pyx_t_5) { - /* "cvcf.pyx":652 + /* "pysam/cvcf.pyx":652 * # gracefully deal with absent FORMAT column * # and those missing samples * if len(cols) == 8: # <<<<<<<<<<<<<< @@ -14687,7 +14869,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_5 = (__pyx_t_4 == 8); if (__pyx_t_5) { - /* "cvcf.pyx":653 + /* "pysam/cvcf.pyx":653 * # and those missing samples * if len(cols) == 8: * cols.append("") # <<<<<<<<<<<<<< @@ -14701,7 +14883,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":655 + /* "pysam/cvcf.pyx":655 * cols.append("") * else: * self.error(line, # <<<<<<<<<<<<<< @@ -14711,7 +14893,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - /* "cvcf.pyx":656 + /* "pysam/cvcf.pyx":656 * else: * self.error(line, * self.BAD_NUMBER_OF_COLUMNS, # <<<<<<<<<<<<<< @@ -14721,7 +14903,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_104); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - /* "cvcf.pyx":657 + /* "pysam/cvcf.pyx":657 * self.error(line, * self.BAD_NUMBER_OF_COLUMNS, * "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols))) # <<<<<<<<<<<<<< @@ -14784,7 +14966,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L3:; - /* "cvcf.pyx":659 + /* "pysam/cvcf.pyx":659 * "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols))) * * chrom = cols[0] # <<<<<<<<<<<<<< @@ -14796,7 +14978,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_chrom = __pyx_t_9; __pyx_t_9 = 0; - /* "cvcf.pyx":662 + /* "pysam/cvcf.pyx":662 * * # get 0-based position * try: pos = int(cols[1])-1 # <<<<<<<<<<<<<< @@ -14838,7 +15020,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; - /* "cvcf.pyx":663 + /* "pysam/cvcf.pyx":663 * # get 0-based position * try: pos = int(cols[1])-1 * except: self.error(line,self.POS_NOT_NUMERICAL) # <<<<<<<<<<<<<< @@ -14846,7 +15028,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * */ /*except:*/ { - __Pyx_AddTraceback("cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;} __Pyx_GOTREF(__pyx_t_10); __Pyx_GOTREF(__pyx_t_9); @@ -14887,7 +15069,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_L12_try_end:; } - /* "cvcf.pyx":664 + /* "pysam/cvcf.pyx":664 * try: pos = int(cols[1])-1 * except: self.error(line,self.POS_NOT_NUMERICAL) * if pos < 0: self.error(line,self.POS_NOT_POSITIVE) # <<<<<<<<<<<<<< @@ -14895,8 +15077,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * # implement filtering */ if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_2 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_5) { @@ -14921,7 +15102,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L15:; - /* "cvcf.pyx":667 + /* "pysam/cvcf.pyx":667 * * # implement filtering * if not self.inregion(chrom,pos): return None # <<<<<<<<<<<<<< @@ -14954,7 +15135,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L16:; - /* "cvcf.pyx":670 + /* "pysam/cvcf.pyx":670 * * # end of first-pass parse for sortedVCF * if lineparse: return chrom, pos, line # <<<<<<<<<<<<<< @@ -14982,7 +15163,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L17:; - /* "cvcf.pyx":672 + /* "pysam/cvcf.pyx":672 * if lineparse: return chrom, pos, line * * id = cols[2] # <<<<<<<<<<<<<< @@ -14994,7 +15175,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_id = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":674 + /* "pysam/cvcf.pyx":674 * id = cols[2] * * ref = cols[3].upper() # <<<<<<<<<<<<<< @@ -15012,17 +15193,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_ref = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":675 + /* "pysam/cvcf.pyx":675 * * ref = cols[3].upper() * if ref == ".": # <<<<<<<<<<<<<< * self.error(line,self.MISSING_REF) * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) */ - __pyx_t_14 = __Pyx_PyString_Equals(__pyx_v_ref, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_RichCompare(__pyx_v_ref, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_14) { - /* "cvcf.pyx":676 + /* "pysam/cvcf.pyx":676 * ref = cols[3].upper() * if ref == ".": * self.error(line,self.MISSING_REF) # <<<<<<<<<<<<<< @@ -15047,7 +15230,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - /* "cvcf.pyx":677 + /* "pysam/cvcf.pyx":677 * if ref == ".": * self.error(line,self.MISSING_REF) * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) # <<<<<<<<<<<<<< @@ -15056,8 +15239,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; @@ -15093,7 +15275,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":678 + /* "pysam/cvcf.pyx":678 * self.error(line,self.MISSING_REF) * if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) * else: ref = "" # <<<<<<<<<<<<<< @@ -15109,7 +15291,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":680 + /* "pysam/cvcf.pyx":680 * else: ref = "" * else: * for c in ref: # <<<<<<<<<<<<<< @@ -15127,10 +15309,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ for (;;) { if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_8 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; - __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_8 = __pyx_t_15(__pyx_t_2); if (unlikely(!__pyx_t_8)) { @@ -15146,14 +15336,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_c = __pyx_t_8; __pyx_t_8 = 0; - /* "cvcf.pyx":681 + /* "pysam/cvcf.pyx":681 * else: * for c in ref: * if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF) # <<<<<<<<<<<<<< * if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference) * */ - __pyx_t_14 = (__Pyx_NegateNonNeg(PySequence_Contains(((PyObject *)__pyx_n_s__ACGTN), __pyx_v_c))); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = (__Pyx_PySequence_Contains(__pyx_v_c, ((PyObject *)__pyx_n_s__ACGTN), Py_NE)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_14) { __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); @@ -15178,14 +15368,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":682 + /* "pysam/cvcf.pyx":682 * for c in ref: * if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF) * if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference) # <<<<<<<<<<<<<< * * # make sure reference is sane */ - __pyx_t_14 = ((PySequence_Contains(__pyx_v_ref, ((PyObject *)__pyx_n_s__N)))); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__N), __pyx_v_ref, Py_EQ)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_14) { __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -15224,7 +15414,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L18:; - /* "cvcf.pyx":685 + /* "pysam/cvcf.pyx":685 * * # make sure reference is sane * if self._reference: # <<<<<<<<<<<<<< @@ -15237,7 +15427,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_14) { - /* "cvcf.pyx":686 + /* "pysam/cvcf.pyx":686 * # make sure reference is sane * if self._reference: * left = max(0,pos-100) # <<<<<<<<<<<<<< @@ -15249,8 +15439,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_16 = 0; __pyx_t_2 = PyInt_FromLong(__pyx_t_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_GT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_GT); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; @@ -15264,27 +15453,29 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_10 = 0; } __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __Pyx_INCREF(__pyx_t_8); - __pyx_v_left = __pyx_t_8; + __pyx_t_9 = __pyx_t_8; + __Pyx_INCREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_v_left = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":687 + /* "pysam/cvcf.pyx":687 * if self._reference: * left = max(0,pos-100) * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) # <<<<<<<<<<<<<< * faref = faref_leftflank[pos-left:] * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) */ - __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_chrom); @@ -15295,81 +15486,80 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GIVEREF(__pyx_v_left); PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_10); __Pyx_GIVEREF(__pyx_t_10); - PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8); + __Pyx_GIVEREF(__pyx_t_8); __pyx_t_10 = 0; - __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = 0; + __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_v_faref_leftflank = __pyx_t_9; - __pyx_t_9 = 0; + __pyx_v_faref_leftflank = __pyx_t_8; + __pyx_t_8 = 0; - /* "cvcf.pyx":688 + /* "pysam/cvcf.pyx":688 * left = max(0,pos-100) * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) * faref = faref_leftflank[pos-left:] # <<<<<<<<<<<<<< * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) * ref = faref */ - __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_faref_leftflank, __pyx_t_4, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_v_faref = __pyx_t_9; - __pyx_t_9 = 0; + __pyx_t_8 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_8); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_faref_leftflank, __pyx_t_4, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_v_faref = __pyx_t_8; + __pyx_t_8 = 0; - /* "cvcf.pyx":689 + /* "pysam/cvcf.pyx":689 * faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) * faref = faref_leftflank[pos-left:] * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) # <<<<<<<<<<<<<< * ref = faref * */ - __pyx_t_9 = PyObject_RichCompare(__pyx_v_faref, __pyx_v_ref, Py_NE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_8 = PyObject_RichCompare(__pyx_v_faref, __pyx_v_ref, Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (__pyx_t_14) { - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__WRONG_REF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_INCREF(__pyx_v_faref); - PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_faref); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_faref); __Pyx_GIVEREF(__pyx_v_faref); __Pyx_INCREF(__pyx_v_ref); - PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_ref); + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_ref); __Pyx_GIVEREF(__pyx_v_ref); - __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_106), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_106), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_10)); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_8, 2, ((PyObject *)__pyx_t_10)); + PyTuple_SET_ITEM(__pyx_t_9, 2, ((PyObject *)__pyx_t_10)); __Pyx_GIVEREF(((PyObject *)__pyx_t_10)); __pyx_t_2 = 0; __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; goto __pyx_L25; } __pyx_L25:; - /* "cvcf.pyx":690 + /* "pysam/cvcf.pyx":690 * faref = faref_leftflank[pos-left:] * if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) * ref = faref # <<<<<<<<<<<<<< @@ -15383,7 +15573,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L24:; - /* "cvcf.pyx":693 + /* "pysam/cvcf.pyx":693 * * # convert v3.3 to v4.0 alleles below * if cols[4] == ".": alt = [] # <<<<<<<<<<<<<< @@ -15392,55 +15582,59 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_14) { - __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_GIVEREF(((PyObject *)__pyx_t_10)); - __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_10); - __pyx_t_10 = 0; + __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_GIVEREF(((PyObject *)__pyx_t_9)); + __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_9); + __pyx_t_9 = 0; goto __pyx_L26; } /*else*/ { - /* "cvcf.pyx":694 + /* "pysam/cvcf.pyx":694 * # convert v3.3 to v4.0 alleles below * if cols[4] == ".": alt = [] * else: alt = cols[4].upper().split(',') # <<<<<<<<<<<<<< * * if cols[5] == ".": qual = -1 */ - __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_8 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __Pyx_GIVEREF(__pyx_t_10); - __pyx_cur_scope->__pyx_v_alt = __pyx_t_10; - __pyx_t_10 = 0; + __Pyx_GIVEREF(__pyx_t_9); + __pyx_cur_scope->__pyx_v_alt = __pyx_t_9; + __pyx_t_9 = 0; } __pyx_L26:; - /* "cvcf.pyx":696 + /* "pysam/cvcf.pyx":696 * else: alt = cols[4].upper().split(',') * * if cols[5] == ".": qual = -1 # <<<<<<<<<<<<<< * else: * try: qual = float(cols[5]) */ - __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_14) { __pyx_v_qual = -1.0; @@ -15448,7 +15642,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":698 + /* "pysam/cvcf.pyx":698 * if cols[5] == ".": qual = -1 * else: * try: qual = float(cols[5]) # <<<<<<<<<<<<<< @@ -15476,11 +15670,11 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; - /* "cvcf.pyx":699 + /* "pysam/cvcf.pyx":699 * else: * try: qual = float(cols[5]) * except: self.error(line,self.QUAL_NOT_NUMERICAL) # <<<<<<<<<<<<<< @@ -15488,11 +15682,11 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * # postpone checking that filters exist. Encode missing filter or no filtering as empty list */ /*except:*/ { - __Pyx_AddTraceback("cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_GOTREF(__pyx_t_8); __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(__pyx_t_8); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;} @@ -15511,8 +15705,8 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; goto __pyx_L29_exception_handled; } __pyx_L30_except_error:; @@ -15531,26 +15725,32 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L27:; - /* "cvcf.pyx":702 + /* "pysam/cvcf.pyx":702 * * # postpone checking that filters exist. Encode missing filter or no filtering as empty list * if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] # <<<<<<<<<<<<<< * else: filter = cols[6].split(';') * */ - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (!__pyx_t_14) { __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__PASS), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__PASS), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (!__pyx_t_5) { - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_18 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s__0), Py_EQ); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_kp_s__0), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_18 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_19 = __pyx_t_18; } else { @@ -15569,7 +15769,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":703 + /* "pysam/cvcf.pyx":703 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list * if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] * else: filter = cols[6].split(';') # <<<<<<<<<<<<<< @@ -15589,7 +15789,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L38:; - /* "cvcf.pyx":706 + /* "pysam/cvcf.pyx":706 * * # dictionary of keys, and list of values * info = {} # <<<<<<<<<<<<<< @@ -15601,7 +15801,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_info = __pyx_t_9; __pyx_t_9 = 0; - /* "cvcf.pyx":707 + /* "pysam/cvcf.pyx":707 * # dictionary of keys, and list of values * info = {} * if cols[7] != ".": # <<<<<<<<<<<<<< @@ -15610,73 +15810,83 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_NE); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (__pyx_t_5) { - /* "cvcf.pyx":708 + /* "pysam/cvcf.pyx":708 * info = {} * if cols[7] != ".": * for blurp in cols[7].split(';'): # <<<<<<<<<<<<<< * elts = blurp.split('=') * if len(elts) == 1: v = None */ - __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_8 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_109), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) { - __pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_109), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) { + __pyx_t_9 = __pyx_t_8; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext; } - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_9 = __pyx_t_15(__pyx_t_8); - if (unlikely(!__pyx_t_9)) { + __pyx_t_8 = __pyx_t_15(__pyx_t_9); + if (unlikely(!__pyx_t_8)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(__pyx_t_8); } __Pyx_XDECREF(__pyx_v_blurp); - __pyx_v_blurp = __pyx_t_9; - __pyx_t_9 = 0; + __pyx_v_blurp = __pyx_t_8; + __pyx_t_8 = 0; - /* "cvcf.pyx":709 + /* "pysam/cvcf.pyx":709 * if cols[7] != ".": * for blurp in cols[7].split(';'): * elts = blurp.split('=') # <<<<<<<<<<<<<< * if len(elts) == 1: v = None * elif len(elts) == 2: v = elts[1] */ - __pyx_t_9 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_110), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_110), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_XDECREF(__pyx_v_elts); __pyx_v_elts = __pyx_t_10; __pyx_t_10 = 0; - /* "cvcf.pyx":710 + /* "pysam/cvcf.pyx":710 * for blurp in cols[7].split(';'): * elts = blurp.split('=') * if len(elts) == 1: v = None # <<<<<<<<<<<<<< @@ -15692,7 +15902,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ goto __pyx_L42; } - /* "cvcf.pyx":711 + /* "pysam/cvcf.pyx":711 * elts = blurp.split('=') * if len(elts) == 1: v = None * elif len(elts) == 2: v = elts[1] # <<<<<<<<<<<<<< @@ -15711,7 +15921,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":712 + /* "pysam/cvcf.pyx":712 * if len(elts) == 1: v = None * elif len(elts) == 2: v = elts[1] * else: self.error(line,self.ERROR_INFO_STRING) # <<<<<<<<<<<<<< @@ -15720,37 +15930,37 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); - __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_8); + __Pyx_GIVEREF(__pyx_t_8); + __pyx_t_8 = 0; + __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; } __pyx_L42:; - /* "cvcf.pyx":713 + /* "pysam/cvcf.pyx":713 * elif len(elts) == 2: v = elts[1] * else: self.error(line,self.ERROR_INFO_STRING) * info[elts[0]] = self.parse_formatdata(elts[0], # <<<<<<<<<<<<<< * v, * self._info, */ - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - /* "cvcf.pyx":714 + /* "pysam/cvcf.pyx":714 * else: self.error(line,self.ERROR_INFO_STRING) * info[elts[0]] = self.parse_formatdata(elts[0], * v, # <<<<<<<<<<<<<< @@ -15759,7 +15969,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ if (unlikely(!__pyx_v_v)) { __Pyx_RaiseUnboundLocalError("v"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 714; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "cvcf.pyx":715 + /* "pysam/cvcf.pyx":715 * info[elts[0]] = self.parse_formatdata(elts[0], * v, * self._info, # <<<<<<<<<<<<<< @@ -15769,7 +15979,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - /* "cvcf.pyx":716 + /* "pysam/cvcf.pyx":716 * v, * self._info, * line) # <<<<<<<<<<<<<< @@ -15790,12 +16000,12 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GIVEREF(__pyx_v_line); __pyx_t_7 = 0; __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":713 + /* "pysam/cvcf.pyx":713 * elif len(elts) == 2: v = elts[1] * else: self.error(line,self.ERROR_INFO_STRING) * info[elts[0]] = self.parse_formatdata(elts[0], # <<<<<<<<<<<<<< @@ -15808,52 +16018,54 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L39; } __pyx_L39:; - /* "cvcf.pyx":719 + /* "pysam/cvcf.pyx":719 * * # Gracefully deal with absent FORMAT column * if cols[8] == "": format = [] # <<<<<<<<<<<<<< * else: format = cols[8].split(':') * */ - __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_kp_s_1), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_1), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_5) { - __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_v_format = ((PyObject *)__pyx_t_8); - __pyx_t_8 = 0; + __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_v_format = ((PyObject *)__pyx_t_10); + __pyx_t_10 = 0; goto __pyx_L43; } /*else*/ { - /* "cvcf.pyx":720 + /* "pysam/cvcf.pyx":720 * # Gracefully deal with absent FORMAT column * if cols[8] == "": format = [] * else: format = cols[8].split(':') # <<<<<<<<<<<<<< * * # check: all filters are defined */ - __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_10 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__split); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_111), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_v_format = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_111), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_v_format = __pyx_t_10; + __pyx_t_10 = 0; } __pyx_L43:; - /* "cvcf.pyx":723 + /* "pysam/cvcf.pyx":723 * * # check: all filters are defined * for f in filter: # <<<<<<<<<<<<<< @@ -15861,87 +16073,95 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * */ if (PyList_CheckExact(__pyx_v_filter) || PyTuple_CheckExact(__pyx_v_filter)) { - __pyx_t_8 = __pyx_v_filter; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __pyx_t_10 = __pyx_v_filter; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_filter); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_v_filter); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_10 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_10 = __pyx_t_15(__pyx_t_8); - if (unlikely(!__pyx_t_10)) { + __pyx_t_9 = __pyx_t_15(__pyx_t_10); + if (unlikely(!__pyx_t_9)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_10); + __Pyx_GOTREF(__pyx_t_9); } __Pyx_XDECREF(__pyx_v_f); - __pyx_v_f = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_f = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":724 + /* "pysam/cvcf.pyx":724 * # check: all filters are defined * for f in filter: * if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f) # <<<<<<<<<<<<<< * * # check: format fields are defined */ - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_5 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_10, __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_9, Py_NE)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_5) { - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FILTER_NOT_DEFINED); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_f); - PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_v_f); + PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_v_f); __Pyx_GIVEREF(__pyx_v_f); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L46; } __pyx_L46:; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - /* "cvcf.pyx":727 + /* "pysam/cvcf.pyx":727 * * # check: format fields are defined * if self._format: # <<<<<<<<<<<<<< * for f in format: * if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f) */ - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_5) { - /* "cvcf.pyx":728 + /* "pysam/cvcf.pyx":728 * # check: format fields are defined * if self._format: * for f in format: # <<<<<<<<<<<<<< @@ -15949,22 +16169,30 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * */ if (PyList_CheckExact(__pyx_v_format) || PyTuple_CheckExact(__pyx_v_format)) { - __pyx_t_8 = __pyx_v_format; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __pyx_t_10 = __pyx_v_format; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_v_format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_1 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_1 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_1 = __pyx_t_15(__pyx_t_8); + __pyx_t_1 = __pyx_t_15(__pyx_t_10); if (unlikely(!__pyx_t_1)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); @@ -15978,7 +16206,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_f = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":729 + /* "pysam/cvcf.pyx":729 * if self._format: * for f in format: * if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f) # <<<<<<<<<<<<<< @@ -15987,55 +16215,54 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_1, __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_1, Py_NE)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_5) { __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FORMAT_NOT_DEFINED); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FORMAT_NOT_DEFINED); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8); + __Pyx_GIVEREF(__pyx_t_8); __Pyx_INCREF(__pyx_v_f); - PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_v_f); + PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_v_f); __Pyx_GIVEREF(__pyx_v_f); - __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = 0; + __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; goto __pyx_L50; } __pyx_L50:; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; goto __pyx_L47; } __pyx_L47:; - /* "cvcf.pyx":732 + /* "pysam/cvcf.pyx":732 * * # convert v3.3 alleles * if self._version == 33: # <<<<<<<<<<<<<< * if len(ref) != 1: self.error(line,self.V33_BAD_REF) * newalts = [] */ - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_8 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_5) { - /* "cvcf.pyx":733 + /* "pysam/cvcf.pyx":733 * # convert v3.3 alleles * if self._version == 33: * if len(ref) != 1: self.error(line,self.V33_BAD_REF) # <<<<<<<<<<<<<< @@ -16045,40 +16272,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_5 = (__pyx_t_4 != 1); if (__pyx_t_5) { - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_REF); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); - __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_REF); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_8); - __Pyx_GIVEREF(__pyx_t_8); - __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_10); + __Pyx_GIVEREF(__pyx_t_10); + __pyx_t_10 = 0; + __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; goto __pyx_L52; } __pyx_L52:; - /* "cvcf.pyx":734 + /* "pysam/cvcf.pyx":734 * if self._version == 33: * if len(ref) != 1: self.error(line,self.V33_BAD_REF) * newalts = [] # <<<<<<<<<<<<<< * have_deletions = False * for a in alt: */ - __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_v_newalts = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_v_newalts = __pyx_t_10; + __pyx_t_10 = 0; - /* "cvcf.pyx":735 + /* "pysam/cvcf.pyx":735 * if len(ref) != 1: self.error(line,self.V33_BAD_REF) * newalts = [] * have_deletions = False # <<<<<<<<<<<<<< @@ -16087,7 +16314,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_v_have_deletions = 0; - /* "cvcf.pyx":736 + /* "pysam/cvcf.pyx":736 * newalts = [] * have_deletions = False * for a in alt: # <<<<<<<<<<<<<< @@ -16095,36 +16322,44 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference */ if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __pyx_t_10 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_10 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_10 = __pyx_t_15(__pyx_t_8); - if (unlikely(!__pyx_t_10)) { + __pyx_t_9 = __pyx_t_15(__pyx_t_10); + if (unlikely(!__pyx_t_9)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_10); + __Pyx_GOTREF(__pyx_t_9); } __Pyx_XDECREF(__pyx_v_a); - __pyx_v_a = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_a = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":737 + /* "pysam/cvcf.pyx":737 * have_deletions = False * for a in alt: * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference # <<<<<<<<<<<<<< @@ -16134,69 +16369,69 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_3 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_5 = (__pyx_t_3 == 1); if (__pyx_t_5) { - __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_9 = PyNumber_Add(__pyx_v_a, __pyx_t_10); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_8 = PyNumber_Add(__pyx_v_a, __pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_v_a); - __pyx_v_a = __pyx_t_9; - __pyx_t_9 = 0; + __pyx_v_a = __pyx_t_8; + __pyx_t_8 = 0; goto __pyx_L55; } - /* "cvcf.pyx":738 + /* "pysam/cvcf.pyx":738 * for a in alt: * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference # <<<<<<<<<<<<<< * elif a.startswith('D'): # allow D and D * have_deletions = True */ - __pyx_t_9 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_5) { - __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_1 = PyNumber_Add(__pyx_t_10, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_1 = PyNumber_Add(__pyx_t_9, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyNumber_Add(__pyx_t_1, __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyNumber_Add(__pyx_t_1, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_v_a); - __pyx_v_a = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_a = __pyx_t_9; + __pyx_t_9 = 0; goto __pyx_L55; } - /* "cvcf.pyx":739 + /* "pysam/cvcf.pyx":739 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference * elif a.startswith('D'): # allow D and D # <<<<<<<<<<<<<< * have_deletions = True * try: */ - __pyx_t_10 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_113), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_113), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (__pyx_t_5) { - /* "cvcf.pyx":740 + /* "pysam/cvcf.pyx":740 * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference * elif a.startswith('D'): # allow D and D * have_deletions = True # <<<<<<<<<<<<<< @@ -16205,7 +16440,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_v_have_deletions = 1; - /* "cvcf.pyx":741 + /* "pysam/cvcf.pyx":741 * elif a.startswith('D'): # allow D and D * have_deletions = True * try: # <<<<<<<<<<<<<< @@ -16219,28 +16454,28 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_XGOTREF(__pyx_t_13); /*try:*/ { - /* "cvcf.pyx":742 + /* "pysam/cvcf.pyx":742 * have_deletions = True * try: * l = int(a[1:]) # throws ValueError if sequence # <<<<<<<<<<<<<< * if len(ref) < l: # add to reference if necessary * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) */ - __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_10); - PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); - __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;} __Pyx_GOTREF(__pyx_t_9); - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8); + __Pyx_GIVEREF(__pyx_t_8); + __pyx_t_8 = 0; + __pyx_t_8 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __Pyx_XDECREF(__pyx_v_l); - __pyx_v_l = __pyx_t_9; - __pyx_t_9 = 0; + __pyx_v_l = __pyx_t_8; + __pyx_t_8 = 0; - /* "cvcf.pyx":743 + /* "pysam/cvcf.pyx":743 * try: * l = int(a[1:]) # throws ValueError if sequence * if len(ref) < l: # add to reference if necessary # <<<<<<<<<<<<<< @@ -16248,32 +16483,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * ref += addns */ __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_v_l, Py_LT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_v_l, Py_LT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_5) { - /* "cvcf.pyx":744 + /* "pysam/cvcf.pyx":744 * l = int(a[1:]) # throws ValueError if sequence * if len(ref) < l: # add to reference if necessary * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) # <<<<<<<<<<<<<< * ref += addns * for i,na in enumerate(newalts): newalts[i] = na+addns */ - __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} __Pyx_GOTREF(__pyx_t_9); - __pyx_t_1 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_1 = PyNumber_Add(__pyx_v_pos, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_9 = PyNumber_Add(__pyx_v_pos, __pyx_v_l); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = PyNumber_Add(__pyx_v_pos, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} @@ -16283,22 +16517,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GIVEREF(__pyx_v_chrom); PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); - PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_8); + __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_1 = 0; - __pyx_t_9 = 0; + __pyx_t_8 = 0; __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;} __Pyx_GOTREF(__pyx_t_7); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_v_addns); __pyx_v_addns = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":745 + /* "pysam/cvcf.pyx":745 * if len(ref) < l: # add to reference if necessary * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) * ref += addns # <<<<<<<<<<<<<< @@ -16311,7 +16545,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_ref = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":746 + /* "pysam/cvcf.pyx":746 * addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) * ref += addns * for i,na in enumerate(newalts): newalts[i] = na+addns # <<<<<<<<<<<<<< @@ -16323,22 +16557,26 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_2 = ((PyObject *)__pyx_v_newalts); __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0; for (;;) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_10); __pyx_t_3++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_9); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + #endif __Pyx_XDECREF(__pyx_v_na); - __pyx_v_na = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_na = __pyx_t_9; + __pyx_t_9 = 0; __Pyx_INCREF(__pyx_t_7); __Pyx_XDECREF(__pyx_v_i); __pyx_v_i = __pyx_t_7; - __pyx_t_10 = PyNumber_Add(__pyx_t_7, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyNumber_Add(__pyx_t_7, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_7); - __pyx_t_7 = __pyx_t_10; - __pyx_t_10 = 0; - __pyx_t_10 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_GOTREF(__pyx_t_10); - if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_7 = __pyx_t_9; + __pyx_t_9 = 0; + __pyx_t_9 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_GOTREF(__pyx_t_9); + if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -16346,7 +16584,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L64:; - /* "cvcf.pyx":747 + /* "pysam/cvcf.pyx":747 * ref += addns * for i,na in enumerate(newalts): newalts[i] = na+addns * a = ref[l:] # new deletion, deleting pos...pos+l # <<<<<<<<<<<<<< @@ -16367,12 +16605,12 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_L56_error:; __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; + __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; - __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; - /* "cvcf.pyx":748 + /* "pysam/cvcf.pyx":748 * for i,na in enumerate(newalts): newalts[i] = na+addns * a = ref[l:] # new deletion, deleting pos...pos+l * except ValueError: # <<<<<<<<<<<<<< @@ -16381,26 +16619,26 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_20 = PyErr_ExceptionMatches(__pyx_builtin_ValueError); if (__pyx_t_20) { - __Pyx_AddTraceback("cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_2, &__pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_2, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_GOTREF(__pyx_t_2); - __Pyx_GOTREF(__pyx_t_10); + __Pyx_GOTREF(__pyx_t_9); - /* "cvcf.pyx":749 + /* "pysam/cvcf.pyx":749 * a = ref[l:] # new deletion, deleting pos...pos+l * except ValueError: * s = a[1:] # <<<<<<<<<<<<<< * if len(ref) < len(s): # add Ns to reference if necessary * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) */ - __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_XDECREF(__pyx_v_s); - __pyx_v_s = __pyx_t_9; - __pyx_t_9 = 0; + __pyx_v_s = __pyx_t_8; + __pyx_t_8 = 0; - /* "cvcf.pyx":750 + /* "pysam/cvcf.pyx":750 * except ValueError: * s = a[1:] * if len(ref) < len(s): # add Ns to reference if necessary # <<<<<<<<<<<<<< @@ -16412,15 +16650,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_5 = (__pyx_t_3 < __pyx_t_21); if (__pyx_t_5) { - /* "cvcf.pyx":751 + /* "pysam/cvcf.pyx":751 * s = a[1:] * if len(ref) < len(s): # add Ns to reference if necessary * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) # <<<<<<<<<<<<<< * if not s.endswith(addns) and addns != 'N'*len(addns): * self.error(line,self.V33_UNMATCHED_DELETION, */ - __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_GOTREF(__pyx_t_8); __pyx_t_21 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __Pyx_GOTREF(__pyx_t_1); @@ -16449,15 +16687,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_6 = 0; __pyx_t_22 = 0; __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __pyx_t_1 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0; __Pyx_XDECREF(__pyx_v_addns); __pyx_v_addns = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":752 + /* "pysam/cvcf.pyx":752 * if len(ref) < len(s): # add Ns to reference if necessary * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) * if not s.endswith(addns) and addns != 'N'*len(addns): # <<<<<<<<<<<<<< @@ -16471,41 +16709,43 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_INCREF(__pyx_v_addns); PyTuple_SET_ITEM(__pyx_t_23, 0, __pyx_v_addns); __Pyx_GIVEREF(__pyx_v_addns); - __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_GOTREF(__pyx_t_9); + __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_14 = (!__pyx_t_5); if (__pyx_t_14) { __pyx_t_21 = PyObject_Length(__pyx_v_addns); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_GOTREF(__pyx_t_9); - __pyx_t_23 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_9); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_23 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_8); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_23)); - __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_addns, ((PyObject *)__pyx_t_23), Py_NE); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_8 = PyObject_RichCompare(__pyx_v_addns, ((PyObject *)__pyx_t_23), Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_19 = __pyx_t_5; } else { __pyx_t_19 = __pyx_t_14; } if (__pyx_t_19) { - /* "cvcf.pyx":753 + /* "pysam/cvcf.pyx":753 * addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) * if not s.endswith(addns) and addns != 'N'*len(addns): * self.error(line,self.V33_UNMATCHED_DELETION, # <<<<<<<<<<<<<< * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) * ref += addns */ - __pyx_t_23 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_23 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_114); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __Pyx_GOTREF(__pyx_t_23); - __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_114); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_GOTREF(__pyx_t_9); - /* "cvcf.pyx":754 + /* "pysam/cvcf.pyx":754 * if not s.endswith(addns) and addns != 'N'*len(addns): * self.error(line,self.V33_UNMATCHED_DELETION, * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) # <<<<<<<<<<<<<< @@ -16556,22 +16796,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_INCREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_9); - __Pyx_GIVEREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_23); + __Pyx_GIVEREF(__pyx_t_23); PyTuple_SET_ITEM(__pyx_t_24, 2, ((PyObject *)__pyx_t_22)); __Pyx_GIVEREF(((PyObject *)__pyx_t_22)); - __pyx_t_9 = 0; + __pyx_t_23 = 0; __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(__pyx_t_23, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __pyx_t_22 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L70; } __pyx_L70:; - /* "cvcf.pyx":755 + /* "pysam/cvcf.pyx":755 * self.error(line,self.V33_UNMATCHED_DELETION, * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) * ref += addns # <<<<<<<<<<<<<< @@ -16584,7 +16824,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_ref = __pyx_t_22; __pyx_t_22 = 0; - /* "cvcf.pyx":756 + /* "pysam/cvcf.pyx":756 * "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) * ref += addns * for i,na in enumerate(newalts): newalts[i] = na+addns # <<<<<<<<<<<<<< @@ -16596,22 +16836,26 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_24 = ((PyObject *)__pyx_v_newalts); __Pyx_INCREF(__pyx_t_24); __pyx_t_21 = 0; for (;;) { if (__pyx_t_21 >= PyList_GET_SIZE(__pyx_t_24)) break; - __pyx_t_23 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_21); __Pyx_INCREF(__pyx_t_23); __pyx_t_21++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_21); __Pyx_INCREF(__pyx_t_8); __pyx_t_21++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_24, __pyx_t_21); __pyx_t_21++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + #endif __Pyx_XDECREF(__pyx_v_na); - __pyx_v_na = __pyx_t_23; - __pyx_t_23 = 0; + __pyx_v_na = __pyx_t_8; + __pyx_t_8 = 0; __Pyx_INCREF(__pyx_t_22); __Pyx_XDECREF(__pyx_v_i); __pyx_v_i = __pyx_t_22; - __pyx_t_23 = PyNumber_Add(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_GOTREF(__pyx_t_23); + __pyx_t_8 = PyNumber_Add(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_22); - __pyx_t_22 = __pyx_t_23; - __pyx_t_23 = 0; - __pyx_t_23 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_GOTREF(__pyx_t_23); - if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_23) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __pyx_t_22 = __pyx_t_8; + __pyx_t_8 = 0; + __pyx_t_8 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_GOTREF(__pyx_t_8); + if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; } __Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0; __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; @@ -16619,7 +16863,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L69:; - /* "cvcf.pyx":757 + /* "pysam/cvcf.pyx":757 * ref += addns * for i,na in enumerate(newalts): newalts[i] = na+addns * a = ref[len(s):] # new deletion, deleting from pos # <<<<<<<<<<<<<< @@ -16634,7 +16878,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_22 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L57_exception_handled; } __pyx_L58_except_error:; @@ -16654,15 +16898,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":759 + /* "pysam/cvcf.pyx":759 * a = ref[len(s):] # new deletion, deleting from pos * else: * self.error(line,self.V33_BAD_ALLELE) # <<<<<<<<<<<<<< * newalts.append(a) * alt = newalts */ - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_ALLELE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -16673,15 +16917,15 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; } __pyx_L55:; - /* "cvcf.pyx":760 + /* "pysam/cvcf.pyx":760 * else: * self.error(line,self.V33_BAD_ALLELE) * newalts.append(a) # <<<<<<<<<<<<<< @@ -16690,9 +16934,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_25 = PyList_Append(__pyx_v_newalts, __pyx_v_a); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - /* "cvcf.pyx":761 + /* "pysam/cvcf.pyx":761 * self.error(line,self.V33_BAD_ALLELE) * newalts.append(a) * alt = newalts # <<<<<<<<<<<<<< @@ -16705,7 +16949,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GIVEREF(((PyObject *)__pyx_v_newalts)); __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_v_newalts); - /* "cvcf.pyx":763 + /* "pysam/cvcf.pyx":763 * alt = newalts * # deletion alleles exist, add dummy 1st reference allele, and account for leading base * if have_deletions: # <<<<<<<<<<<<<< @@ -16714,28 +16958,27 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ if (__pyx_v_have_deletions) { - /* "cvcf.pyx":764 + /* "pysam/cvcf.pyx":764 * # deletion alleles exist, add dummy 1st reference allele, and account for leading base * if have_deletions: * if pos == 0: # <<<<<<<<<<<<<< * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) */ - __pyx_t_8 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_10 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_19) { - /* "cvcf.pyx":766 + /* "pysam/cvcf.pyx":766 * if pos == 0: * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) # <<<<<<<<<<<<<< * ref += addn * alt = [allele+addn for allele in alt] */ - __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -16745,14 +16988,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyNumber_Add(__pyx_t_10, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __pyx_t_22 = PyTuple_New(4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); __Pyx_INCREF(__pyx_v_chrom); @@ -16762,40 +17005,40 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_t_10); - __Pyx_GIVEREF(__pyx_t_10); + PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_t_9); + __Pyx_GIVEREF(__pyx_t_9); __pyx_t_7 = 0; __pyx_t_2 = 0; - __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; - __pyx_v_addn = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_addn = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":767 + /* "pysam/cvcf.pyx":767 * # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) * ref += addn # <<<<<<<<<<<<<< * alt = [allele+addn for allele in alt] * else: */ - __pyx_t_10 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addn); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addn); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_v_ref); - __pyx_v_ref = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_ref = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":768 + /* "pysam/cvcf.pyx":768 * addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) * ref += addn * alt = [allele+addn for allele in alt] # <<<<<<<<<<<<<< * else: * addn = get_sequence(chrom,pos-1,pos,self._reference) */ - __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0; __pyx_t_15 = NULL; @@ -16807,96 +17050,106 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ for (;;) { if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break; - __pyx_t_8 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_22, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break; - __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_22, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_8 = __pyx_t_15(__pyx_t_22); - if (unlikely(!__pyx_t_8)) { + __pyx_t_10 = __pyx_t_15(__pyx_t_22); + if (unlikely(!__pyx_t_10)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(__pyx_t_10); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_8; - __pyx_t_8 = 0; - __pyx_t_8 = PyNumber_Add(__pyx_v_allele, __pyx_v_addn); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - if (unlikely(PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_8))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_v_allele = __pyx_t_10; + __pyx_t_10 = 0; + __pyx_t_10 = PyNumber_Add(__pyx_v_allele, __pyx_v_addn); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; } __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __Pyx_INCREF(((PyObject *)__pyx_t_10)); + __pyx_t_22 = ((PyObject *)__pyx_t_9); + __Pyx_INCREF(__pyx_t_22); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt); __Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt); - __Pyx_GIVEREF(((PyObject *)__pyx_t_10)); - __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_10); - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; + __Pyx_GIVEREF(__pyx_t_22); + __pyx_cur_scope->__pyx_v_alt = __pyx_t_22; + __pyx_t_22 = 0; goto __pyx_L74; } /*else*/ { - /* "cvcf.pyx":770 + /* "pysam/cvcf.pyx":770 * alt = [allele+addn for allele in alt] * else: * addn = get_sequence(chrom,pos-1,pos,self._reference) # <<<<<<<<<<<<<< * ref = addn + ref * alt = [addn + allele for allele in alt] */ - __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_22 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_chrom); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_chrom); __Pyx_GIVEREF(__pyx_v_chrom); - PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_22); - __Pyx_GIVEREF(__pyx_t_22); + PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_9); + __Pyx_GIVEREF(__pyx_t_9); __Pyx_INCREF(__pyx_v_pos); PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_pos); __Pyx_GIVEREF(__pyx_v_pos); - PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8); - __Pyx_GIVEREF(__pyx_t_8); - __pyx_t_22 = 0; - __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_10); + __Pyx_GIVEREF(__pyx_t_10); + __pyx_t_9 = 0; + __pyx_t_10 = 0; + __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_v_addn = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_addn = __pyx_t_10; + __pyx_t_10 = 0; - /* "cvcf.pyx":771 + /* "pysam/cvcf.pyx":771 * else: * addn = get_sequence(chrom,pos-1,pos,self._reference) * ref = addn + ref # <<<<<<<<<<<<<< * alt = [addn + allele for allele in alt] * pos -= 1 */ - __pyx_t_8 = PyNumber_Add(__pyx_v_addn, __pyx_v_ref); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_10 = PyNumber_Add(__pyx_v_addn, __pyx_v_ref); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_v_ref); - __pyx_v_ref = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_ref = __pyx_t_10; + __pyx_t_10 = 0; - /* "cvcf.pyx":772 + /* "pysam/cvcf.pyx":772 * addn = get_sequence(chrom,pos-1,pos,self._reference) * ref = addn + ref * alt = [addn + allele for allele in alt] # <<<<<<<<<<<<<< * pos -= 1 * else: */ - __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0; __pyx_t_15 = NULL; @@ -16908,49 +17161,59 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ for (;;) { if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; - __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_22 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_22 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; - __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_22 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_10 = __pyx_t_15(__pyx_t_2); - if (unlikely(!__pyx_t_10)) { + __pyx_t_22 = __pyx_t_15(__pyx_t_2); + if (unlikely(!__pyx_t_22)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_10); + __Pyx_GOTREF(__pyx_t_22); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_10; - __pyx_t_10 = 0; - __pyx_t_10 = PyNumber_Add(__pyx_v_addn, __pyx_v_allele); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_v_allele = __pyx_t_22; + __pyx_t_22 = 0; + __pyx_t_22 = PyNumber_Add(__pyx_v_addn, __pyx_v_allele); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + if (unlikely(__Pyx_PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_22))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_INCREF(((PyObject *)__pyx_t_8)); + __pyx_t_2 = ((PyObject *)__pyx_t_10); + __Pyx_INCREF(__pyx_t_2); + __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt); __Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt); - __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); - __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; + __Pyx_GIVEREF(__pyx_t_2); + __pyx_cur_scope->__pyx_v_alt = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":773 + /* "pysam/cvcf.pyx":773 * ref = addn + ref * alt = [addn + allele for allele in alt] * pos -= 1 # <<<<<<<<<<<<<< * else: * # format v4.0 -- just check for nucleotides */ - __pyx_t_8 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_pos); - __pyx_v_pos = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_pos = __pyx_t_2; + __pyx_t_2 = 0; } __pyx_L74:; goto __pyx_L73; @@ -16960,7 +17223,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":776 + /* "pysam/cvcf.pyx":776 * else: * # format v4.0 -- just check for nucleotides * for allele in alt: # <<<<<<<<<<<<<< @@ -16968,97 +17231,105 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * self.error(line,self.V40_BAD_ALLELE,allele) */ if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_2 = __pyx_t_15(__pyx_t_8); - if (unlikely(!__pyx_t_2)) { + __pyx_t_10 = __pyx_t_15(__pyx_t_2); + if (unlikely(!__pyx_t_10)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_10); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_2; - __pyx_t_2 = 0; + __pyx_v_allele = __pyx_t_10; + __pyx_t_10 = 0; - /* "cvcf.pyx":777 + /* "pysam/cvcf.pyx":777 * # format v4.0 -- just check for nucleotides * for allele in alt: * if not alleleRegEx.match(allele): # <<<<<<<<<<<<<< * self.error(line,self.V40_BAD_ALLELE,allele) * */ - __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__alleleRegEx); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__match); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__alleleRegEx); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_INCREF(__pyx_v_allele); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_allele); - __Pyx_GIVEREF(__pyx_v_allele); - __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__match); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __Pyx_INCREF(__pyx_v_allele); + PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_allele); + __Pyx_GIVEREF(__pyx_v_allele); + __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; + __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_14 = (!__pyx_t_19); if (__pyx_t_14) { - /* "cvcf.pyx":778 + /* "pysam/cvcf.pyx":778 * for allele in alt: * if not alleleRegEx.match(allele): * self.error(line,self.V40_BAD_ALLELE,allele) # <<<<<<<<<<<<<< * * # check for leading nucleotide in indel calls */ - __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V40_BAD_ALLELE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V40_BAD_ALLELE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); + __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_10); + __Pyx_GIVEREF(__pyx_t_10); __Pyx_INCREF(__pyx_v_allele); - PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_v_allele); + PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_v_allele); __Pyx_GIVEREF(__pyx_v_allele); - __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_10 = 0; + __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; goto __pyx_L81; } __pyx_L81:; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; } __pyx_L51:; - /* "cvcf.pyx":781 + /* "pysam/cvcf.pyx":781 * * # check for leading nucleotide in indel calls * for allele in alt: # <<<<<<<<<<<<<< @@ -17066,36 +17337,44 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) */ if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_2 = __pyx_t_15(__pyx_t_8); - if (unlikely(!__pyx_t_2)) { + __pyx_t_10 = __pyx_t_15(__pyx_t_2); + if (unlikely(!__pyx_t_10)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_10); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_2; - __pyx_t_2 = 0; + __pyx_v_allele = __pyx_t_10; + __pyx_t_10 = 0; - /* "cvcf.pyx":782 + /* "pysam/cvcf.pyx":782 * # check for leading nucleotide in indel calls * for allele in alt: * if len(allele) != len(ref): # <<<<<<<<<<<<<< @@ -17107,7 +17386,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_14 = (__pyx_t_21 != __pyx_t_3); if (__pyx_t_14) { - /* "cvcf.pyx":783 + /* "pysam/cvcf.pyx":783 * for allele in alt: * if len(allele) != len(ref): * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) # <<<<<<<<<<<<<< @@ -17117,103 +17396,102 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_3 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = (__pyx_t_3 == 0); if (__pyx_t_14) { - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ZERO_LENGTH_ALLELE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_22 = PyTuple_New(2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ZERO_LENGTH_ALLELE); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_10); - __Pyx_GIVEREF(__pyx_t_10); - __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_22); + __Pyx_GIVEREF(__pyx_t_22); + __pyx_t_22 = 0; + __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; goto __pyx_L85; } __pyx_L85:; - /* "cvcf.pyx":784 + /* "pysam/cvcf.pyx":784 * if len(allele) != len(ref): * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): # <<<<<<<<<<<<<< * self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) * */ - __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_2 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_RichCompare(__pyx_t_10, __pyx_t_22, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_9, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_14) { - __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_10 = PyNumber_Add(__pyx_t_2, __pyx_t_22); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_22 = PyNumber_Add(__pyx_t_10, __pyx_t_9); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_19 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__N), __pyx_t_22, Py_NE)); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_19 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_10, ((PyObject *)__pyx_n_s__N)))); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_5 = __pyx_t_19; } else { __pyx_t_5 = __pyx_t_14; } if (__pyx_t_5) { - /* "cvcf.pyx":785 + /* "pysam/cvcf.pyx":785 * if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) * if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): * self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) # <<<<<<<<<<<<<< * * # trim trailing bases in alleles */ - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_116); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_116); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_22); - __Pyx_GIVEREF(__pyx_t_22); - __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9); + __Pyx_GIVEREF(__pyx_t_9); + __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; goto __pyx_L86; } __pyx_L86:; @@ -17221,9 +17499,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L84:; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":788 + /* "pysam/cvcf.pyx":788 * * # trim trailing bases in alleles * if alt: # <<<<<<<<<<<<<< @@ -17233,148 +17511,154 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_alt); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_5) { - /* "cvcf.pyx":789 + /* "pysam/cvcf.pyx":789 * # trim trailing bases in alleles * if alt: * for i in range(1,min(len(ref),min(map(len,alt)))): # <<<<<<<<<<<<<< * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): * break */ - __pyx_t_8 = __Pyx_GetName(__pyx_b, __pyx_n_s__len); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_22 = PyTuple_New(2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_8); - __Pyx_GIVEREF(__pyx_t_8); + __pyx_t_2 = __Pyx_GetName(__pyx_b, __pyx_n_s__len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); __Pyx_INCREF(__pyx_cur_scope->__pyx_v_alt); - PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_cur_scope->__pyx_v_alt); + PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_cur_scope->__pyx_v_alt); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_alt); - __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; - __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_8); - __Pyx_GIVEREF(__pyx_t_8); - __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; - __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyObject_RichCompare(__pyx_t_8, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_RichCompare(__pyx_t_2, __pyx_t_10, Py_LT); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; if (__pyx_t_5) { - __Pyx_INCREF(__pyx_t_8); - __pyx_t_22 = __pyx_t_8; + __Pyx_INCREF(__pyx_t_2); + __pyx_t_9 = __pyx_t_2; } else { - __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_22 = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __pyx_t_9 = __pyx_t_22; + __pyx_t_22 = 0; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_INCREF(__pyx_int_1); - PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_int_1); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_int_1); __Pyx_GIVEREF(__pyx_int_1); - __Pyx_INCREF(__pyx_t_22); - PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_22); - __Pyx_GIVEREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - if (PyList_CheckExact(__pyx_t_22) || PyTuple_CheckExact(__pyx_t_22)) { - __pyx_t_8 = __pyx_t_22; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __Pyx_INCREF(__pyx_t_9); + PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_9); + __Pyx_GIVEREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) { + __pyx_t_2 = __pyx_t_9; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext; } - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_22 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_22 = __pyx_t_15(__pyx_t_8); - if (unlikely(!__pyx_t_22)) { + __pyx_t_9 = __pyx_t_15(__pyx_t_2); + if (unlikely(!__pyx_t_9)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_22); + __Pyx_GOTREF(__pyx_t_9); } __Pyx_XDECREF(__pyx_v_i); - __pyx_v_i = __pyx_t_22; - __pyx_t_22 = 0; + __pyx_v_i = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":790 + /* "pysam/cvcf.pyx":790 * if alt: * for i in range(1,min(len(ref),min(map(len,alt)))): * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<< * break * ref, alt = ref[:-1], [allele[:-1] for allele in alt] */ - __pyx_t_22 = __pyx_pf_4cvcf_3VCF_10parse_data_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_22); - __Pyx_GIVEREF(__pyx_t_22); - __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(((PyObject *)((PyObject*)(&PySet_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __pyx_t_3 = PySet_Size(__pyx_t_22); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_9); + __Pyx_GIVEREF(__pyx_t_9); + __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PySet_Type))), ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; + __pyx_t_3 = PySet_Size(__pyx_t_9); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_5 = (__pyx_t_3 > 1); if (!__pyx_t_5) { - __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_ref, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_ref, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_22 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_alt, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_alt, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_22, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_10, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_RichCompare(__pyx_t_9, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __pyx_t_19 = __pyx_t_14; } else { __pyx_t_19 = __pyx_t_5; } if (__pyx_t_19) { - /* "cvcf.pyx":791 + /* "pysam/cvcf.pyx":791 * for i in range(1,min(len(ref),min(map(len,alt)))): * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): * break # <<<<<<<<<<<<<< @@ -17386,34 +17670,42 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L90:; - /* "cvcf.pyx":792 + /* "pysam/cvcf.pyx":792 * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): * break * ref, alt = ref[:-1], [allele[:-1] for allele in alt] # <<<<<<<<<<<<<< * * # left-align alleles, if a reference is available */ - __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_3 = 0; + __pyx_t_9 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_9); __pyx_t_3 = 0; __pyx_t_26 = NULL; } else { - __pyx_t_3 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_26 = Py_TYPE(__pyx_t_22)->tp_iternext; + __pyx_t_3 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_26 = Py_TYPE(__pyx_t_9)->tp_iternext; } for (;;) { - if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_22)) { - if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_22)) break; - __pyx_t_7 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; - } else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_22)) { - if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_22)) break; - __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; + if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_9)) { + if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_9, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_9)) { + if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_9, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_7 = __pyx_t_26(__pyx_t_22); + __pyx_t_7 = __pyx_t_26(__pyx_t_9); if (unlikely(!__pyx_t_7)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); @@ -17428,51 +17720,51 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_7 = 0; __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - if (unlikely(PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; } - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = ((PyObject *)__pyx_t_2); - __Pyx_INCREF(__pyx_t_22); - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = ((PyObject *)__pyx_t_10); + __Pyx_INCREF(__pyx_t_9); + __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; __Pyx_DECREF(__pyx_v_ref); - __pyx_v_ref = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_ref = __pyx_t_22; + __pyx_t_22 = 0; __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt); __Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt); - __Pyx_GIVEREF(__pyx_t_22); - __pyx_cur_scope->__pyx_v_alt = __pyx_t_22; - __pyx_t_22 = 0; + __Pyx_GIVEREF(__pyx_t_9); + __pyx_cur_scope->__pyx_v_alt = __pyx_t_9; + __pyx_t_9 = 0; } __pyx_L89_break:; - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L87; } __pyx_L87:; - /* "cvcf.pyx":795 + /* "pysam/cvcf.pyx":795 * * # left-align alleles, if a reference is available * if self._leftalign and self._reference: # <<<<<<<<<<<<<< * while left < pos: * movable = True */ - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_19) { - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_14 = __pyx_t_5; } else { __pyx_t_14 = __pyx_t_19; } if (__pyx_t_14) { - /* "cvcf.pyx":796 + /* "pysam/cvcf.pyx":796 * # left-align alleles, if a reference is available * if self._leftalign and self._reference: * while left < pos: # <<<<<<<<<<<<<< @@ -17481,13 +17773,12 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ while (1) { if (unlikely(!__pyx_v_left)) { __Pyx_RaiseUnboundLocalError("left"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_8 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_2 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (!__pyx_t_14) break; - /* "cvcf.pyx":797 + /* "pysam/cvcf.pyx":797 * if self._leftalign and self._reference: * while left < pos: * movable = True # <<<<<<<<<<<<<< @@ -17496,7 +17787,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_v_movable = 1; - /* "cvcf.pyx":798 + /* "pysam/cvcf.pyx":798 * while left < pos: * movable = True * for allele in alt: # <<<<<<<<<<<<<< @@ -17504,36 +17795,44 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * longest, shortest = allele, ref */ if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0; + __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break; - __pyx_t_22 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break; - __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_22 = __pyx_t_15(__pyx_t_8); - if (unlikely(!__pyx_t_22)) { + __pyx_t_9 = __pyx_t_15(__pyx_t_2); + if (unlikely(!__pyx_t_9)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_22); + __Pyx_GOTREF(__pyx_t_9); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_22; - __pyx_t_22 = 0; + __pyx_v_allele = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":799 + /* "pysam/cvcf.pyx":799 * movable = True * for allele in alt: * if len(allele) > len(ref): # <<<<<<<<<<<<<< @@ -17545,48 +17844,48 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_14 = (__pyx_t_3 > __pyx_t_21); if (__pyx_t_14) { - /* "cvcf.pyx":800 + /* "pysam/cvcf.pyx":800 * for allele in alt: * if len(allele) > len(ref): * longest, shortest = allele, ref # <<<<<<<<<<<<<< * else: * longest, shortest = ref, allele */ - __pyx_t_22 = __pyx_v_allele; + __pyx_t_9 = __pyx_v_allele; + __Pyx_INCREF(__pyx_t_9); + __pyx_t_22 = __pyx_v_ref; __Pyx_INCREF(__pyx_t_22); - __pyx_t_10 = __pyx_v_ref; - __Pyx_INCREF(__pyx_t_10); __Pyx_XDECREF(__pyx_v_longest); - __pyx_v_longest = __pyx_t_22; - __pyx_t_22 = 0; + __pyx_v_longest = __pyx_t_9; + __pyx_t_9 = 0; __Pyx_XDECREF(__pyx_v_shortest); - __pyx_v_shortest = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_shortest = __pyx_t_22; + __pyx_t_22 = 0; goto __pyx_L98; } /*else*/ { - /* "cvcf.pyx":802 + /* "pysam/cvcf.pyx":802 * longest, shortest = allele, ref * else: * longest, shortest = ref, allele # <<<<<<<<<<<<<< * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): * movable = False */ - __pyx_t_10 = __pyx_v_ref; - __Pyx_INCREF(__pyx_t_10); - __pyx_t_22 = __pyx_v_allele; + __pyx_t_22 = __pyx_v_ref; __Pyx_INCREF(__pyx_t_22); + __pyx_t_9 = __pyx_v_allele; + __Pyx_INCREF(__pyx_t_9); __Pyx_XDECREF(__pyx_v_longest); - __pyx_v_longest = __pyx_t_10; - __pyx_t_10 = 0; - __Pyx_XDECREF(__pyx_v_shortest); - __pyx_v_shortest = __pyx_t_22; + __pyx_v_longest = __pyx_t_22; __pyx_t_22 = 0; + __Pyx_XDECREF(__pyx_v_shortest); + __pyx_v_shortest = __pyx_t_9; + __pyx_t_9 = 0; } __pyx_L98:; - /* "cvcf.pyx":803 + /* "pysam/cvcf.pyx":803 * else: * longest, shortest = ref, allele * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): # <<<<<<<<<<<<<< @@ -17598,32 +17897,31 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_14 = (__pyx_t_21 == __pyx_t_3); if (!__pyx_t_14) { __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_longest, 0, __pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_longest, 0, __pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_22 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetAttr(__pyx_v_shortest, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_GetAttr(__pyx_v_shortest, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_RichCompare(__pyx_t_9, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __pyx_t_5 = __pyx_t_19; } else { __pyx_t_5 = __pyx_t_14; } if (__pyx_t_5) { - /* "cvcf.pyx":804 + /* "pysam/cvcf.pyx":804 * longest, shortest = ref, allele * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): * movable = False # <<<<<<<<<<<<<< @@ -17635,40 +17933,39 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L99:; - /* "cvcf.pyx":805 + /* "pysam/cvcf.pyx":805 * if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): * movable = False * if longest[-1].upper() != longest[len(shortest)-1].upper(): # <<<<<<<<<<<<<< * movable = False * if not movable: */ - __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_longest, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_longest, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_2 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_21 = (__pyx_t_3 - 1); - __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_longest, __pyx_t_21, sizeof(Py_ssize_t), PyInt_FromSsize_t); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_22 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_RichCompare(__pyx_t_10, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); + __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_longest, __pyx_t_21, sizeof(Py_ssize_t), PyInt_FromSsize_t); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_9 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_RichCompare(__pyx_t_22, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; if (__pyx_t_5) { - /* "cvcf.pyx":806 + /* "pysam/cvcf.pyx":806 * movable = False * if longest[-1].upper() != longest[len(shortest)-1].upper(): * movable = False # <<<<<<<<<<<<<< @@ -17680,9 +17977,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L100:; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":807 + /* "pysam/cvcf.pyx":807 * if longest[-1].upper() != longest[len(shortest)-1].upper(): * movable = False * if not movable: # <<<<<<<<<<<<<< @@ -17692,7 +17989,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_5 = (!__pyx_v_movable); if (__pyx_t_5) { - /* "cvcf.pyx":808 + /* "pysam/cvcf.pyx":808 * movable = False * if not movable: * break # <<<<<<<<<<<<<< @@ -17704,129 +18001,146 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L101:; - /* "cvcf.pyx":809 + /* "pysam/cvcf.pyx":809 * if not movable: * break * ref = ref[:-1] # <<<<<<<<<<<<<< * alt = [allele[:-1] for allele in alt] * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: */ - __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_ref); - __pyx_v_ref = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_ref = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":810 + /* "pysam/cvcf.pyx":810 * break * ref = ref[:-1] * alt = [allele[:-1] for allele in alt] # <<<<<<<<<<<<<< * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: * ref = faref_leftflank[pos-left-1] + ref */ - __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0; + __pyx_t_9 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_2 = __pyx_t_15(__pyx_t_22); - if (unlikely(!__pyx_t_2)) { + __pyx_t_10 = __pyx_t_15(__pyx_t_9); + if (unlikely(!__pyx_t_10)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_10); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_2; - __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_2))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_v_allele = __pyx_t_10; + __pyx_t_10 = 0; + __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + if (unlikely(__Pyx_PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; } - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __Pyx_INCREF(((PyObject *)__pyx_t_8)); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = ((PyObject *)__pyx_t_2); + __Pyx_INCREF(__pyx_t_9); + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt); __Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt); - __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); - __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; + __Pyx_GIVEREF(__pyx_t_9); + __pyx_cur_scope->__pyx_v_alt = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":811 + /* "pysam/cvcf.pyx":811 * ref = ref[:-1] * alt = [allele[:-1] for allele in alt] * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: # <<<<<<<<<<<<<< * ref = faref_leftflank[pos-left-1] + ref * alt = [faref_leftflank[pos-left-1] + allele for allele in alt] */ - __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0; + __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_2 = __pyx_t_15(__pyx_t_22); - if (unlikely(!__pyx_t_2)) { + __pyx_t_10 = __pyx_t_15(__pyx_t_2); + if (unlikely(!__pyx_t_10)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_10); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_2; - __pyx_t_2 = 0; + __pyx_v_allele = __pyx_t_10; + __pyx_t_10 = 0; __pyx_t_21 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_2))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; } - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __Pyx_INCREF(((PyObject *)__pyx_t_8)); - PyTuple_SET_ITEM(__pyx_t_22, 0, ((PyObject *)__pyx_t_8)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_RichCompare(__pyx_t_8, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_INCREF(((PyObject *)__pyx_t_9)); + PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_9)); + __Pyx_GIVEREF(((PyObject *)__pyx_t_9)); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (!__pyx_t_5) { __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_14 = (__pyx_t_4 == 0); @@ -17836,7 +18150,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } if (__pyx_t_19) { - /* "cvcf.pyx":812 + /* "pysam/cvcf.pyx":812 * alt = [allele[:-1] for allele in alt] * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: * ref = faref_leftflank[pos-left-1] + ref # <<<<<<<<<<<<<< @@ -17844,93 +18158,103 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * pos -= 1 */ if (unlikely(!__pyx_v_faref_leftflank)) { __Pyx_RaiseUnboundLocalError("faref_leftflank"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_22 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_8 = PyNumber_Subtract(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_22 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_8); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = PyNumber_Add(__pyx_t_22, __pyx_v_ref); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_2 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_9 = PyNumber_Subtract(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_9); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_9 = PyNumber_Add(__pyx_t_2, __pyx_v_ref); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_v_ref); - __pyx_v_ref = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_ref = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":813 + /* "pysam/cvcf.pyx":813 * if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: * ref = faref_leftflank[pos-left-1] + ref * alt = [faref_leftflank[pos-left-1] + allele for allele in alt] # <<<<<<<<<<<<<< * pos -= 1 * */ - __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) { - __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0; + __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_2 = __pyx_t_15(__pyx_t_22); - if (unlikely(!__pyx_t_2)) { + __pyx_t_10 = __pyx_t_15(__pyx_t_2); + if (unlikely(!__pyx_t_10)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(__pyx_t_10); } __Pyx_XDECREF(__pyx_v_allele); - __pyx_v_allele = __pyx_t_2; - __pyx_t_2 = 0; - __pyx_t_2 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyNumber_Subtract(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_allele = __pyx_t_10; + __pyx_t_10 = 0; + __pyx_t_10 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_10); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_22 = PyNumber_Subtract(__pyx_t_10, __pyx_int_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyNumber_Add(__pyx_t_2, __pyx_v_allele); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_22); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyNumber_Add(__pyx_t_10, __pyx_v_allele); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_22))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; } - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __Pyx_INCREF(((PyObject *)__pyx_t_8)); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = ((PyObject *)__pyx_t_9); + __Pyx_INCREF(__pyx_t_2); + __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt); __Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt); - __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); - __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8); - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; + __Pyx_GIVEREF(__pyx_t_2); + __pyx_cur_scope->__pyx_v_alt = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":814 + /* "pysam/cvcf.pyx":814 * ref = faref_leftflank[pos-left-1] + ref * alt = [faref_leftflank[pos-left-1] + allele for allele in alt] * pos -= 1 # <<<<<<<<<<<<<< * * # parse sample columns */ - __pyx_t_8 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_v_pos); - __pyx_v_pos = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_pos = __pyx_t_2; + __pyx_t_2 = 0; goto __pyx_L104; } __pyx_L104:; @@ -17940,88 +18264,96 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L93:; - /* "cvcf.pyx":817 + /* "pysam/cvcf.pyx":817 * * # parse sample columns * samples = [] # <<<<<<<<<<<<<< * for sample in cols[9:]: * dict = {} */ - __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_v_samples = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_v_samples = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":818 + /* "pysam/cvcf.pyx":818 * # parse sample columns * samples = [] * for sample in cols[9:]: # <<<<<<<<<<<<<< * dict = {} * values = sample.split(':') */ - __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_cols, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) { - __pyx_t_22 = __pyx_t_8; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0; + __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_cols, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) { + __pyx_t_9 = __pyx_t_2; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); - __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext; + __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext; } - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break; - __pyx_t_8 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) { - if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break; - __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) { + if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) { + if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_8 = __pyx_t_15(__pyx_t_22); - if (unlikely(!__pyx_t_8)) { + __pyx_t_2 = __pyx_t_15(__pyx_t_9); + if (unlikely(!__pyx_t_2)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(__pyx_t_2); } __Pyx_XDECREF(__pyx_v_sample); - __pyx_v_sample = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_sample = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":819 + /* "pysam/cvcf.pyx":819 * samples = [] * for sample in cols[9:]: * dict = {} # <<<<<<<<<<<<<< * values = sample.split(':') * if len(values) > len(format): */ - __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_8)); + __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_XDECREF(((PyObject *)__pyx_v_dict)); - __pyx_v_dict = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_dict = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":820 + /* "pysam/cvcf.pyx":820 * for sample in cols[9:]: * dict = {} * values = sample.split(':') # <<<<<<<<<<<<<< * if len(values) > len(format): * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) */ - __pyx_t_8 = PyObject_GetAttr(__pyx_v_sample, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + __pyx_t_2 = PyObject_GetAttr(__pyx_v_sample, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_22 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_v_values); - __pyx_v_values = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_values = __pyx_t_22; + __pyx_t_22 = 0; - /* "cvcf.pyx":821 + /* "pysam/cvcf.pyx":821 * dict = {} * values = sample.split(':') * if len(values) > len(format): # <<<<<<<<<<<<<< @@ -18033,33 +18365,33 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_19 = (__pyx_t_21 > __pyx_t_3); if (__pyx_t_19) { - /* "cvcf.pyx":822 + /* "pysam/cvcf.pyx":822 * values = sample.split(':') * if len(values) > len(format): * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) # <<<<<<<<<<<<<< * for idx in range(len(format)): * expected = self.get_expected(format[idx], self._format, alt) */ - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_18); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_18); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_24); - PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_10); + __Pyx_GIVEREF(__pyx_t_10); __Pyx_INCREF(__pyx_v_sample); PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_v_sample); __Pyx_GIVEREF(__pyx_v_sample); PyTuple_SET_ITEM(__pyx_t_24, 2, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); - __pyx_t_2 = 0; + __pyx_t_10 = 0; __pyx_t_7 = 0; __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), ((PyObject *)__pyx_t_24)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_7)); @@ -18069,22 +18401,22 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_INCREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_8); - __Pyx_GIVEREF(__pyx_t_8); + PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_24, 2, ((PyObject *)__pyx_t_7)); __Pyx_GIVEREF(((PyObject *)__pyx_t_7)); - __pyx_t_8 = 0; + __pyx_t_2 = 0; __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; goto __pyx_L111; } __pyx_L111:; - /* "cvcf.pyx":823 + /* "pysam/cvcf.pyx":823 * if len(values) > len(format): * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) * for idx in range(len(format)): # <<<<<<<<<<<<<< @@ -18114,10 +18446,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ for (;;) { if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_24)) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_24)) break; - __pyx_t_7 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_24, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_24)) { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_24)) break; - __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_7 = PySequence_ITEM(__pyx_t_24, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_7 = __pyx_t_26(__pyx_t_24); if (unlikely(!__pyx_t_7)) { @@ -18133,7 +18473,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_idx = __pyx_t_7; __pyx_t_7 = 0; - /* "cvcf.pyx":824 + /* "pysam/cvcf.pyx":824 * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) * for idx in range(len(format)): * expected = self.get_expected(format[idx], self._format, alt) # <<<<<<<<<<<<<< @@ -18142,30 +18482,30 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__get_expected); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_10); - __Pyx_GIVEREF(__pyx_t_10); - PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_8); - __Pyx_GIVEREF(__pyx_t_8); + __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_22); + __Pyx_GIVEREF(__pyx_t_22); + PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); __Pyx_INCREF(__pyx_cur_scope->__pyx_v_alt); - PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_cur_scope->__pyx_v_alt); + PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_cur_scope->__pyx_v_alt); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_alt); - __pyx_t_10 = 0; - __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_22 = 0; + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; __Pyx_XDECREF(__pyx_v_expected); - __pyx_v_expected = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_expected = __pyx_t_2; + __pyx_t_2 = 0; - /* "cvcf.pyx":825 + /* "pysam/cvcf.pyx":825 * for idx in range(len(format)): * expected = self.get_expected(format[idx], self._format, alt) * if idx < len(values): value = values[idx] # <<<<<<<<<<<<<< @@ -18173,34 +18513,32 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ * if expected == -1: value = "." */ __pyx_t_21 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_8, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_19) { - __pyx_t_2 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_10 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); __Pyx_XDECREF(__pyx_v_value); - __pyx_v_value = __pyx_t_2; - __pyx_t_2 = 0; + __pyx_v_value = __pyx_t_10; + __pyx_t_10 = 0; goto __pyx_L114; } /*else*/ { - /* "cvcf.pyx":827 + /* "pysam/cvcf.pyx":827 * if idx < len(values): value = values[idx] * else: * if expected == -1: value = "." # <<<<<<<<<<<<<< * else: value = ",".join(["."]*expected) * */ - __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_10 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_19) { __Pyx_INCREF(((PyObject *)__pyx_kp_s_9)); __Pyx_XDECREF(__pyx_v_value); @@ -18209,288 +18547,285 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":828 + /* "pysam/cvcf.pyx":828 * else: * if expected == -1: value = "." * else: value = ",".join(["."]*expected) # <<<<<<<<<<<<<< * * dict[format[idx]] = self.parse_formatdata(format[idx], */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_8 = PyList_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); __Pyx_INCREF(((PyObject *)__pyx_kp_s_9)); - PyList_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_kp_s_9)); + PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_9)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9)); - { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_8, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_temp); - __Pyx_DECREF(__pyx_t_8); - __pyx_t_8 = __pyx_temp; + __Pyx_DECREF(__pyx_t_2); + __pyx_t_2 = __pyx_temp; } __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); - __pyx_t_8 = 0; - __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_2)); + __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); + __pyx_t_2 = 0; + __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __Pyx_XDECREF(__pyx_v_value); - __pyx_v_value = __pyx_t_8; - __pyx_t_8 = 0; + __pyx_v_value = __pyx_t_2; + __pyx_t_2 = 0; } __pyx_L115:; } __pyx_L114:; - /* "cvcf.pyx":830 + /* "pysam/cvcf.pyx":830 * else: value = ",".join(["."]*expected) * * dict[format[idx]] = self.parse_formatdata(format[idx], # <<<<<<<<<<<<<< * value, * self._format, */ - __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - /* "cvcf.pyx":832 + /* "pysam/cvcf.pyx":832 * dict[format[idx]] = self.parse_formatdata(format[idx], * value, * self._format, # <<<<<<<<<<<<<< * line) * if expected != -1 and len(dict[format[idx]]) != expected: */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); - /* "cvcf.pyx":833 + /* "pysam/cvcf.pyx":833 * value, * self._format, * line) # <<<<<<<<<<<<<< * if expected != -1 and len(dict[format[idx]]) != expected: * self.error(line,self.BAD_NUMBER_OF_PARAMETERS, */ - __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_7); + __pyx_t_22 = PyTuple_New(4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __Pyx_INCREF(__pyx_v_value); - PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_value); + PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_v_value); __Pyx_GIVEREF(__pyx_v_value); - PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_10); + __Pyx_GIVEREF(__pyx_t_10); __Pyx_INCREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_10, 3, __pyx_v_line); + PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); __pyx_t_7 = 0; - __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; + __pyx_t_10 = 0; + __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_10); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; - /* "cvcf.pyx":830 + /* "pysam/cvcf.pyx":830 * else: value = ",".join(["."]*expected) * * dict[format[idx]] = self.parse_formatdata(format[idx], # <<<<<<<<<<<<<< * value, * self._format, */ - __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_10, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_22, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":834 + /* "pysam/cvcf.pyx":834 * self._format, * line) * if expected != -1 and len(dict[format[idx]]) != expected: # <<<<<<<<<<<<<< * self.error(line,self.BAD_NUMBER_OF_PARAMETERS, * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) */ - __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_10 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (__pyx_t_19) { - __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_2); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_21 = PyObject_Length(__pyx_t_10); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_10, __pyx_v_expected, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_21 = PyObject_Length(__pyx_t_22); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_14 = __pyx_t_5; } else { __pyx_t_14 = __pyx_t_19; } if (__pyx_t_14) { - /* "cvcf.pyx":835 + /* "pysam/cvcf.pyx":835 * line) * if expected != -1 and len(dict[format[idx]]) != expected: * self.error(line,self.BAD_NUMBER_OF_PARAMETERS, # <<<<<<<<<<<<<< * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_20); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); + __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_20); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); - /* "cvcf.pyx":836 + /* "pysam/cvcf.pyx":836 * if expected != -1 and len(dict[format[idx]]) != expected: * self.error(line,self.BAD_NUMBER_OF_PARAMETERS, * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) # <<<<<<<<<<<<<< * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) * dict[format[idx]] = dict[format[idx]][:expected] */ - __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_23 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_7); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_23); + __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_7); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8); - __Pyx_GIVEREF(__pyx_t_8); + PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); __Pyx_INCREF(__pyx_v_expected); PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_expected); __Pyx_GIVEREF(__pyx_v_expected); - PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_23); - __Pyx_GIVEREF(__pyx_t_23); + PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_8); + __Pyx_GIVEREF(__pyx_t_8); + __pyx_t_2 = 0; __pyx_t_8 = 0; - __pyx_t_23 = 0; - __pyx_t_23 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_23)); + __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_INCREF(__pyx_v_line); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line); __Pyx_GIVEREF(__pyx_v_line); - PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_10); - __Pyx_GIVEREF(__pyx_t_10); - PyTuple_SET_ITEM(__pyx_t_7, 2, ((PyObject *)__pyx_t_23)); - __Pyx_GIVEREF(((PyObject *)__pyx_t_23)); - __pyx_t_10 = 0; - __pyx_t_23 = 0; - __pyx_t_23 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_23); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_22); + __Pyx_GIVEREF(__pyx_t_22); + PyTuple_SET_ITEM(__pyx_t_7, 2, ((PyObject *)__pyx_t_8)); + __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); + __pyx_t_22 = 0; + __pyx_t_8 = 0; + __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - /* "cvcf.pyx":837 + /* "pysam/cvcf.pyx":837 * self.error(line,self.BAD_NUMBER_OF_PARAMETERS, * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) # <<<<<<<<<<<<<< * dict[format[idx]] = dict[format[idx]][:expected] * samples.append( dict ) */ - __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_23); - __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_21 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_23 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_LT); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_23); + __pyx_t_8 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_23); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (__pyx_t_14) { - __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_23); - __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_2); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_10, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_21 = PyObject_Length(__pyx_t_8); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - __pyx_t_10 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_22, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __pyx_t_8 = PyList_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); - PyList_SET_ITEM(__pyx_t_8, 0, __pyx_t_2); - __Pyx_GIVEREF(__pyx_t_2); - { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_8, __pyx_t_10); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_22); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_21 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __pyx_t_22 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_10); + __Pyx_GIVEREF(__pyx_t_10); + { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_t_22); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_temp); - __Pyx_DECREF(__pyx_t_8); - __pyx_t_8 = __pyx_temp; + __Pyx_DECREF(__pyx_t_2); + __pyx_t_2 = __pyx_temp; } - __pyx_t_2 = 0; - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyNumber_InPlaceAdd(__pyx_t_7, ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __pyx_t_10 = 0; + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyNumber_InPlaceAdd(__pyx_t_7, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_23, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; + if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_8, __pyx_t_22) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; goto __pyx_L117; } __pyx_L117:; - /* "cvcf.pyx":838 + /* "pysam/cvcf.pyx":838 * "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) * dict[format[idx]] = dict[format[idx]][:expected] # <<<<<<<<<<<<<< * samples.append( dict ) * */ - __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_23); - __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __pyx_t_21 = __Pyx_PyIndex_AsSsize_t(__pyx_v_expected); if (unlikely((__pyx_t_21 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_23 = __Pyx_PySequence_GetSlice(__pyx_t_10, 0, __pyx_t_21); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_23); - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); - if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_10, __pyx_t_23) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0; + __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_t_22, 0, __pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_8); + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_22); + if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_22, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; goto __pyx_L116; } __pyx_L116:; } __Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0; - /* "cvcf.pyx":839 + /* "pysam/cvcf.pyx":839 * if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) * dict[format[idx]] = dict[format[idx]][:expected] * samples.append( dict ) # <<<<<<<<<<<<<< @@ -18499,56 +18834,56 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_25 = PyList_Append(__pyx_v_samples, ((PyObject *)__pyx_v_dict)); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - /* "cvcf.pyx":842 + /* "pysam/cvcf.pyx":842 * * # done * d = {'chrom':chrom, # <<<<<<<<<<<<<< * 'pos':pos, # return 0-based position * 'id':id, */ - __pyx_t_22 = PyDict_New(); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_22)); - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__chrom), __pyx_v_chrom) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__chrom), __pyx_v_chrom) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":843 + /* "pysam/cvcf.pyx":843 * # done * d = {'chrom':chrom, * 'pos':pos, # return 0-based position # <<<<<<<<<<<<<< * 'id':id, * 'ref':ref, */ - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__pos), __pyx_v_pos) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__pos), __pyx_v_pos) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":844 + /* "pysam/cvcf.pyx":844 * d = {'chrom':chrom, * 'pos':pos, # return 0-based position * 'id':id, # <<<<<<<<<<<<<< * 'ref':ref, * 'alt':alt, */ - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__id), __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__id), __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":845 + /* "pysam/cvcf.pyx":845 * 'pos':pos, # return 0-based position * 'id':id, * 'ref':ref, # <<<<<<<<<<<<<< * 'alt':alt, * 'qual':qual, */ - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__ref), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__ref), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":846 + /* "pysam/cvcf.pyx":846 * 'id':id, * 'ref':ref, * 'alt':alt, # <<<<<<<<<<<<<< * 'qual':qual, * 'filter':filter, */ - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__alt), __pyx_cur_scope->__pyx_v_alt) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__alt), __pyx_cur_scope->__pyx_v_alt) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":847 + /* "pysam/cvcf.pyx":847 * 'ref':ref, * 'alt':alt, * 'qual':qual, # <<<<<<<<<<<<<< @@ -18557,135 +18892,150 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_24 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_24); - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__qual), __pyx_t_24) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__qual), __pyx_t_24) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0; - /* "cvcf.pyx":848 + /* "pysam/cvcf.pyx":848 * 'alt':alt, * 'qual':qual, * 'filter':filter, # <<<<<<<<<<<<<< * 'info':info, * 'format':format} */ - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__filter), __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__filter), __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":849 + /* "pysam/cvcf.pyx":849 * 'qual':qual, * 'filter':filter, * 'info':info, # <<<<<<<<<<<<<< * 'format':format} * for key,value in zip(self._samples,samples): */ - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__info), ((PyObject *)__pyx_v_info)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__info), ((PyObject *)__pyx_v_info)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":850 + /* "pysam/cvcf.pyx":850 * 'filter':filter, * 'info':info, * 'format':format} # <<<<<<<<<<<<<< * for key,value in zip(self._samples,samples): * d[key] = value */ - if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__format), __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_d = __pyx_t_22; - __pyx_t_22 = 0; + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__format), __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_d = __pyx_t_9; + __pyx_t_9 = 0; - /* "cvcf.pyx":851 + /* "pysam/cvcf.pyx":851 * 'info':info, * 'format':format} * for key,value in zip(self._samples,samples): # <<<<<<<<<<<<<< * d[key] = value * */ - __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __pyx_t_24 = PyTuple_New(2); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_24); - PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_22); - __Pyx_GIVEREF(__pyx_t_22); + PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_9); + __Pyx_GIVEREF(__pyx_t_9); __Pyx_INCREF(((PyObject *)__pyx_v_samples)); PyTuple_SET_ITEM(__pyx_t_24, 1, ((PyObject *)__pyx_v_samples)); __Pyx_GIVEREF(((PyObject *)__pyx_v_samples)); - __pyx_t_22 = 0; - __pyx_t_22 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_22); + __pyx_t_9 = 0; + __pyx_t_9 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0; - if (PyList_CheckExact(__pyx_t_22) || PyTuple_CheckExact(__pyx_t_22)) { - __pyx_t_24 = __pyx_t_22; __Pyx_INCREF(__pyx_t_24); __pyx_t_4 = 0; + if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) { + __pyx_t_24 = __pyx_t_9; __Pyx_INCREF(__pyx_t_24); __pyx_t_4 = 0; __pyx_t_15 = NULL; } else { - __pyx_t_4 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_24); __pyx_t_15 = Py_TYPE(__pyx_t_24)->tp_iternext; } - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; for (;;) { if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_24)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_24)) break; - __pyx_t_22 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_24, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_24)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_24)) break; - __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_9 = PySequence_ITEM(__pyx_t_24, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { - __pyx_t_22 = __pyx_t_15(__pyx_t_24); - if (unlikely(!__pyx_t_22)) { + __pyx_t_9 = __pyx_t_15(__pyx_t_24); + if (unlikely(!__pyx_t_9)) { if (PyErr_Occurred()) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear(); else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } - __Pyx_GOTREF(__pyx_t_22); + __Pyx_GOTREF(__pyx_t_9); } - if ((likely(PyTuple_CheckExact(__pyx_t_22))) || (PyList_CheckExact(__pyx_t_22))) { - PyObject* sequence = __pyx_t_22; + if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) { + PyObject* sequence = __pyx_t_9; + #if CYTHON_COMPILING_IN_CPYTHON + Py_ssize_t size = Py_SIZE(sequence); + #else + Py_ssize_t size = PySequence_Size(sequence); + #endif + if (unlikely(size != 2)) { + if (size > 2) __Pyx_RaiseTooManyValuesError(2); + else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { - if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) { - if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } - __pyx_t_23 = PyTuple_GET_ITEM(sequence, 0); - __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1); + __pyx_t_8 = PyTuple_GET_ITEM(sequence, 0); + __pyx_t_22 = PyTuple_GET_ITEM(sequence, 1); } else { - if (unlikely(PyList_GET_SIZE(sequence) != 2)) { - if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2); - else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence)); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } - __pyx_t_23 = PyList_GET_ITEM(sequence, 0); - __pyx_t_10 = PyList_GET_ITEM(sequence, 1); + __pyx_t_8 = PyList_GET_ITEM(sequence, 0); + __pyx_t_22 = PyList_GET_ITEM(sequence, 1); } - __Pyx_INCREF(__pyx_t_23); - __Pyx_INCREF(__pyx_t_10); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - } else { + __Pyx_INCREF(__pyx_t_8); + __Pyx_INCREF(__pyx_t_22); + #else + __pyx_t_8 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_22 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + } else + { Py_ssize_t index = -1; - __pyx_t_8 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_27 = Py_TYPE(__pyx_t_2)->tp_iternext; + index = 0; __pyx_t_8 = __pyx_t_27(__pyx_t_2); if (unlikely(!__pyx_t_8)) goto __pyx_L120_unpacking_failed; __Pyx_GOTREF(__pyx_t_8); - __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0; - __pyx_t_27 = Py_TYPE(__pyx_t_8)->tp_iternext; - index = 0; __pyx_t_23 = __pyx_t_27(__pyx_t_8); if (unlikely(!__pyx_t_23)) goto __pyx_L120_unpacking_failed; - __Pyx_GOTREF(__pyx_t_23); - index = 1; __pyx_t_10 = __pyx_t_27(__pyx_t_8); if (unlikely(!__pyx_t_10)) goto __pyx_L120_unpacking_failed; - __Pyx_GOTREF(__pyx_t_10); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_27(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; + index = 1; __pyx_t_22 = __pyx_t_27(__pyx_t_2); if (unlikely(!__pyx_t_22)) goto __pyx_L120_unpacking_failed; + __Pyx_GOTREF(__pyx_t_22); + if (__Pyx_IternextUnpackEndCheck(__pyx_t_27(__pyx_t_2), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_27 = NULL; + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L121_unpacking_done; __pyx_L120_unpacking_failed:; - __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); - if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); + __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; + __pyx_t_27 = NULL; + if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L121_unpacking_done:; } __Pyx_XDECREF(__pyx_v_key); - __pyx_v_key = __pyx_t_23; - __pyx_t_23 = 0; + __pyx_v_key = __pyx_t_8; + __pyx_t_8 = 0; __Pyx_XDECREF(__pyx_v_value); - __pyx_v_value = __pyx_t_10; - __pyx_t_10 = 0; + __pyx_v_value = __pyx_t_22; + __pyx_t_22 = 0; - /* "cvcf.pyx":852 + /* "pysam/cvcf.pyx":852 * 'format':format} * for key,value in zip(self._samples,samples): * d[key] = value # <<<<<<<<<<<<<< @@ -18696,7 +19046,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } __Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0; - /* "cvcf.pyx":854 + /* "pysam/cvcf.pyx":854 * d[key] = value * * return d # <<<<<<<<<<<<<< @@ -18721,7 +19071,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_XDECREF(__pyx_t_22); __Pyx_XDECREF(__pyx_t_23); __Pyx_XDECREF(__pyx_t_24); - __Pyx_AddTraceback("cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_cols); @@ -18767,18 +19117,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_35write_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_35write_data = {__Pyx_NAMESTR("write_data"), (PyCFunction)__pyx_pw_4cvcf_3VCF_35write_data, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_35write_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_35write_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_35write_data = {__Pyx_NAMESTR("write_data"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_35write_data, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_35write_data(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; PyObject *__pyx_v_data = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__data,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("write_data (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__data,0}; PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -18793,18 +19142,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_35write_data(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -18827,16 +19173,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_35write_data(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.write_data", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.write_data", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_34write_data(__pyx_self, __pyx_v_self, __pyx_v_stream, __pyx_v_data); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_34write_data(__pyx_self, __pyx_v_self, __pyx_v_stream, __pyx_v_data); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":857 +/* "pysam/cvcf.pyx":857 * * * def write_data(self, stream, data): # <<<<<<<<<<<<<< @@ -18844,7 +19190,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_35write_data(PyObject *__pyx_self, PyObject * for k in required: */ -static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data) { PyObject *__pyx_v_required = NULL; PyObject *__pyx_v_k = NULL; PyObject *__pyx_v_alt = NULL; @@ -18872,7 +19218,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("write_data", 0); - /* "cvcf.pyx":858 + /* "pysam/cvcf.pyx":858 * * def write_data(self, stream, data): * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples # <<<<<<<<<<<<<< @@ -18917,7 +19263,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_required = __pyx_t_3; __pyx_t_3 = 0; - /* "cvcf.pyx":859 + /* "pysam/cvcf.pyx":859 * def write_data(self, stream, data): * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples * for k in required: # <<<<<<<<<<<<<< @@ -18935,10 +19281,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ for (;;) { if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_3)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_3)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_3)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_3)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_2 = __pyx_t_5(__pyx_t_3); if (unlikely(!__pyx_t_2)) { @@ -18954,14 +19308,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_k = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":860 + /* "pysam/cvcf.pyx":860 * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples * for k in required: * if k not in data: raise ValueError("Required key %s not found in data" % str(k)) # <<<<<<<<<<<<<< * if data['alt'] == []: alt = "." * else: alt = ",".join(data['alt']) */ - __pyx_t_6 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_v_data, __pyx_v_k))); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = (__Pyx_PySequence_Contains(__pyx_v_k, __pyx_v_data, Py_NE)); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_6) { __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -18991,7 +19345,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":861 + /* "pysam/cvcf.pyx":861 * for k in required: * if k not in data: raise ValueError("Required key %s not found in data" % str(k)) * if data['alt'] == []: alt = "." # <<<<<<<<<<<<<< @@ -19002,8 +19356,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -19015,7 +19368,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":862 + /* "pysam/cvcf.pyx":862 * if k not in data: raise ValueError("Required key %s not found in data" % str(k)) * if data['alt'] == []: alt = "." * else: alt = ",".join(data['alt']) # <<<<<<<<<<<<<< @@ -19040,7 +19393,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L6:; - /* "cvcf.pyx":863 + /* "pysam/cvcf.pyx":863 * if data['alt'] == []: alt = "." * else: alt = ",".join(data['alt']) * if data['filter'] == None: filter = "." # <<<<<<<<<<<<<< @@ -19049,8 +19402,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -19060,7 +19412,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ goto __pyx_L7; } - /* "cvcf.pyx":864 + /* "pysam/cvcf.pyx":864 * else: alt = ",".join(data['alt']) * if data['filter'] == None: filter = "." * elif data['filter'] == []: # <<<<<<<<<<<<<< @@ -19071,15 +19423,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_6) { - /* "cvcf.pyx":865 + /* "pysam/cvcf.pyx":865 * if data['filter'] == None: filter = "." * elif data['filter'] == []: * if self._version == 33: filter = "0" # <<<<<<<<<<<<<< @@ -19088,8 +19439,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -19100,7 +19450,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":866 + /* "pysam/cvcf.pyx":866 * elif data['filter'] == []: * if self._version == 33: filter = "0" * else: filter = "PASS" # <<<<<<<<<<<<<< @@ -19115,7 +19465,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":867 + /* "pysam/cvcf.pyx":867 * if self._version == 33: filter = "0" * else: filter = "PASS" * else: filter = ';'.join(data['filter']) # <<<<<<<<<<<<<< @@ -19140,7 +19490,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L7:; - /* "cvcf.pyx":868 + /* "pysam/cvcf.pyx":868 * else: filter = "PASS" * else: filter = ';'.join(data['filter']) * if data['qual'] == -1: qual = "." # <<<<<<<<<<<<<< @@ -19149,8 +19499,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ */ __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__qual)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -19161,7 +19510,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } /*else*/ { - /* "cvcf.pyx":869 + /* "pysam/cvcf.pyx":869 * else: filter = ';'.join(data['filter']) * if data['qual'] == -1: qual = "." * else: qual = str(data['qual']) # <<<<<<<<<<<<<< @@ -19183,7 +19532,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L9:; - /* "cvcf.pyx":871 + /* "pysam/cvcf.pyx":871 * else: qual = str(data['qual']) * * output = [data['chrom'], # <<<<<<<<<<<<<< @@ -19193,7 +19542,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__chrom)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - /* "cvcf.pyx":872 + /* "pysam/cvcf.pyx":872 * * output = [data['chrom'], * str(data['pos']+1), # change to 1-based position # <<<<<<<<<<<<<< @@ -19214,7 +19563,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":873 + /* "pysam/cvcf.pyx":873 * output = [data['chrom'], * str(data['pos']+1), # change to 1-based position * data['id'], # <<<<<<<<<<<<<< @@ -19224,7 +19573,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - /* "cvcf.pyx":874 + /* "pysam/cvcf.pyx":874 * str(data['pos']+1), # change to 1-based position * data['id'], * data['ref'], # <<<<<<<<<<<<<< @@ -19234,7 +19583,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_t_7 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__ref)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); - /* "cvcf.pyx":878 + /* "pysam/cvcf.pyx":878 * qual, * filter, * self.format_formatdata( data['info'], self._info, separator=";" ), # <<<<<<<<<<<<<< @@ -19264,7 +19613,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - /* "cvcf.pyx":879 + /* "pysam/cvcf.pyx":879 * filter, * self.format_formatdata( data['info'], self._info, separator=";" ), * self.format_formatdata( data['format'], self._format, value=False ) ] # <<<<<<<<<<<<<< @@ -19328,7 +19677,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_output = __pyx_t_8; __pyx_t_8 = 0; - /* "cvcf.pyx":881 + /* "pysam/cvcf.pyx":881 * self.format_formatdata( data['format'], self._format, value=False ) ] * * for s in self._samples: # <<<<<<<<<<<<<< @@ -19349,10 +19698,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ for (;;) { if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_11)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_11)) break; - __pyx_t_8 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_11)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_11)) break; - __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_8 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_8 = __pyx_t_5(__pyx_t_11); if (unlikely(!__pyx_t_8)) { @@ -19368,7 +19725,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __pyx_v_s = __pyx_t_8; __pyx_t_8 = 0; - /* "cvcf.pyx":882 + /* "pysam/cvcf.pyx":882 * * for s in self._samples: * output.append( self.format_formatdata( data[s], self._format, key=False ) ) # <<<<<<<<<<<<<< @@ -19405,7 +19762,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - /* "cvcf.pyx":884 + /* "pysam/cvcf.pyx":884 * output.append( self.format_formatdata( data[s], self._format, key=False ) ) * * stream.write( "\t".join(output) + "\n" ) # <<<<<<<<<<<<<< @@ -19451,7 +19808,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ __Pyx_XDECREF(__pyx_t_10); __Pyx_XDECREF(__pyx_t_11); __Pyx_XDECREF(__pyx_t_12); - __Pyx_AddTraceback("cvcf.VCF.write_data", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.write_data", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_required); @@ -19467,17 +19824,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_37_parse_header = {__Pyx_NAMESTR("_parse_header"), (PyCFunction)__pyx_pw_4cvcf_3VCF_37_parse_header, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_37_parse_header = {__Pyx_NAMESTR("_parse_header"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("_parse_header (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -19491,12 +19847,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -19517,16 +19871,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF._parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF._parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_36_parse_header(__pyx_self, __pyx_v_self, __pyx_v_stream); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(__pyx_self, __pyx_v_self, __pyx_v_stream); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":886 +/* "pysam/cvcf.pyx":886 * stream.write( "\t".join(output) + "\n" ) * * def _parse_header(self, stream): # <<<<<<<<<<<<<< @@ -19534,7 +19888,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObj * for line in stream: */ -static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { PyObject *__pyx_v_line = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -19550,7 +19904,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_parse_header", 0); - /* "cvcf.pyx":887 + /* "pysam/cvcf.pyx":887 * * def _parse_header(self, stream): * self._lineno = 0 # <<<<<<<<<<<<<< @@ -19559,7 +19913,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p */ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lineno, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":888 + /* "pysam/cvcf.pyx":888 * def _parse_header(self, stream): * self._lineno = 0 * for line in stream: # <<<<<<<<<<<<<< @@ -19577,10 +19931,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p for (;;) { if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_4 = __pyx_t_3(__pyx_t_1); if (unlikely(!__pyx_t_4)) { @@ -19596,7 +19958,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p __pyx_v_line = __pyx_t_4; __pyx_t_4 = 0; - /* "cvcf.pyx":889 + /* "pysam/cvcf.pyx":889 * self._lineno = 0 * for line in stream: * self._lineno += 1 # <<<<<<<<<<<<<< @@ -19611,7 +19973,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lineno, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - /* "cvcf.pyx":890 + /* "pysam/cvcf.pyx":890 * for line in stream: * self._lineno += 1 * if line.startswith('##'): # <<<<<<<<<<<<<< @@ -19627,7 +19989,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_6) { - /* "cvcf.pyx":891 + /* "pysam/cvcf.pyx":891 * self._lineno += 1 * if line.startswith('##'): * self.parse_header( line.strip() ) # <<<<<<<<<<<<<< @@ -19654,7 +20016,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p goto __pyx_L5; } - /* "cvcf.pyx":892 + /* "pysam/cvcf.pyx":892 * if line.startswith('##'): * self.parse_header( line.strip() ) * elif line.startswith('#'): # <<<<<<<<<<<<<< @@ -19670,7 +20032,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_6) { - /* "cvcf.pyx":893 + /* "pysam/cvcf.pyx":893 * self.parse_header( line.strip() ) * elif line.startswith('#'): * self.parse_heading( line.strip() ) # <<<<<<<<<<<<<< @@ -19695,7 +20057,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - /* "cvcf.pyx":894 + /* "pysam/cvcf.pyx":894 * elif line.startswith('#'): * self.parse_heading( line.strip() ) * self.enter_default_format() # <<<<<<<<<<<<<< @@ -19712,7 +20074,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p } /*else*/ { - /* "cvcf.pyx":896 + /* "pysam/cvcf.pyx":896 * self.enter_default_format() * else: * break # <<<<<<<<<<<<<< @@ -19726,7 +20088,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p __pyx_L4_break:; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":897 + /* "pysam/cvcf.pyx":897 * else: * break * return line # <<<<<<<<<<<<<< @@ -19746,7 +20108,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_7); - __Pyx_AddTraceback("cvcf.VCF._parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF._parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_line); @@ -19754,21 +20116,20 @@ static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__p __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ +static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_39_parse = {__Pyx_NAMESTR("_parse"), (PyCFunction)__pyx_pw_4cvcf_3VCF_39_parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_39_parse = {__Pyx_NAMESTR("_parse"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_39_parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_line = 0; PyObject *__pyx_v_stream = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__stream,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("_parse (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__stream,0}; PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -19783,18 +20144,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObject *__ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -19817,16 +20175,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObject *__ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF._parse", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF._parse", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_38_parse(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_stream); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_38_parse(__pyx_self, __pyx_v_self, __pyx_v_line, __pyx_v_stream); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":899 +/* "pysam/cvcf.pyx":899 * return line * * def _parse(self, line, stream): # <<<<<<<<<<<<<< @@ -19834,15 +20192,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObject *__ * if line.startswith("##"): return */ -static PyObject *__pyx_pf_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream) { - struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *__pyx_cur_scope; +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *__pyx_cur_scope; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_parse", 0); - __pyx_cur_scope = (struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)__pyx_ptype_4cvcf___pyx_scope_struct_2__parse->tp_new(__pyx_ptype_4cvcf___pyx_scope_struct_2__parse, __pyx_empty_tuple, NULL); + __pyx_cur_scope = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse->tp_new(__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse, __pyx_empty_tuple, NULL); if (unlikely(!__pyx_cur_scope)) { __Pyx_RefNannyFinishContext(); return NULL; @@ -19858,7 +20216,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self __Pyx_INCREF(__pyx_cur_scope->__pyx_v_stream); __Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_stream); { - __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_4cvcf_3VCF_40generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_4cvcf_3VCF_40generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_cur_scope); __Pyx_RefNannyFinishContext(); return (PyObject *) gen; @@ -19867,7 +20225,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF._parse", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF._parse", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_DECREF(((PyObject *)__pyx_cur_scope)); @@ -19876,9 +20234,9 @@ static PyObject *__pyx_pf_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self return __pyx_r; } -static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */ +static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */ { - struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *__pyx_cur_scope = ((struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)__pyx_generator->closure); + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *__pyx_cur_scope = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)__pyx_generator->closure); PyObject *__pyx_r = NULL; PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; @@ -19902,7 +20260,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge __pyx_L3_first_run:; if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":901 + /* "pysam/cvcf.pyx":901 * def _parse(self, line, stream): * # deal with files with header only * if line.startswith("##"): return # <<<<<<<<<<<<<< @@ -19924,7 +20282,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge } __pyx_L4:; - /* "cvcf.pyx":902 + /* "pysam/cvcf.pyx":902 * # deal with files with header only * if line.startswith("##"): return * if len(line.strip()) > 0: # <<<<<<<<<<<<<< @@ -19941,7 +20299,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge __pyx_t_3 = (__pyx_t_4 > 0); if (__pyx_t_3) { - /* "cvcf.pyx":903 + /* "pysam/cvcf.pyx":903 * if line.startswith("##"): return * if len(line.strip()) > 0: * d = self.parse_data( line.strip() ) # <<<<<<<<<<<<<< @@ -19968,7 +20326,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge __pyx_cur_scope->__pyx_v_d = __pyx_t_5; __pyx_t_5 = 0; - /* "cvcf.pyx":904 + /* "pysam/cvcf.pyx":904 * if len(line.strip()) > 0: * d = self.parse_data( line.strip() ) * if d: yield d # <<<<<<<<<<<<<< @@ -19993,7 +20351,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge } __pyx_L5:; - /* "cvcf.pyx":905 + /* "pysam/cvcf.pyx":905 * d = self.parse_data( line.strip() ) * if d: yield d * for line in stream: # <<<<<<<<<<<<<< @@ -20011,10 +20369,18 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge for (;;) { if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_5)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_5)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_5)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_5)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_2 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_2)) { @@ -20032,7 +20398,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge __pyx_cur_scope->__pyx_v_line = __pyx_t_2; __pyx_t_2 = 0; - /* "cvcf.pyx":906 + /* "pysam/cvcf.pyx":906 * if d: yield d * for line in stream: * self._lineno += 1 # <<<<<<<<<<<<<< @@ -20047,7 +20413,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge if (PyObject_SetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lineno, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":907 + /* "pysam/cvcf.pyx":907 * for line in stream: * self._lineno += 1 * if self._lines and self._lineno > self._lines: raise StopIteration # <<<<<<<<<<<<<< @@ -20063,8 +20429,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lines); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_GT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_GT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -20080,7 +20445,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge } __pyx_L10:; - /* "cvcf.pyx":908 + /* "pysam/cvcf.pyx":908 * self._lineno += 1 * if self._lines and self._lineno > self._lines: raise StopIteration * d = self.parse_data( line.strip() ) # <<<<<<<<<<<<<< @@ -20109,7 +20474,7 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge __pyx_cur_scope->__pyx_v_d = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":909 + /* "pysam/cvcf.pyx":909 * if self._lines and self._lineno > self._lines: raise StopIteration * d = self.parse_data( line.strip() ) * if d: yield d # <<<<<<<<<<<<<< @@ -20152,25 +20517,25 @@ static PyObject *__pyx_gb_4cvcf_3VCF_40generator(__pyx_GeneratorObject *__pyx_ge __pyx_L0:; __Pyx_XDECREF(__pyx_r); __pyx_generator->resume_label = -1; + __Pyx_Generator_clear((PyObject*)__pyx_generator); __Pyx_RefNannyFinishContext(); return NULL; } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_42getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_41getsamples[] = " List of samples in VCF file "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_42getsamples = {__Pyx_NAMESTR("getsamples"), (PyCFunction)__pyx_pw_4cvcf_3VCF_42getsamples, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_41getsamples)}; -static PyObject *__pyx_pw_4cvcf_3VCF_42getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_42getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_41getsamples[] = " List of samples in VCF file "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_42getsamples = {__Pyx_NAMESTR("getsamples"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_42getsamples, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_41getsamples)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_42getsamples(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("getsamples (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_4cvcf_3VCF_41getsamples(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_41getsamples(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":917 +/* "pysam/cvcf.pyx":917 * ###################################################################################################### * * def getsamples(self): # <<<<<<<<<<<<<< @@ -20178,7 +20543,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_42getsamples(PyObject *__pyx_self, PyObject * return self._samples */ -static PyObject *__pyx_pf_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -20187,7 +20552,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("getsamples", 0); - /* "cvcf.pyx":919 + /* "pysam/cvcf.pyx":919 * def getsamples(self): * """ List of samples in VCF file """ * return self._samples # <<<<<<<<<<<<<< @@ -20205,7 +20570,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.getsamples", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.getsamples", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20214,18 +20579,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_43setsamples[] = " List of samples in VCF file "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_44setsamples = {__Pyx_NAMESTR("setsamples"), (PyCFunction)__pyx_pw_4cvcf_3VCF_44setsamples, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_43setsamples)}; -static PyObject *__pyx_pw_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_43setsamples[] = " List of samples in VCF file "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_44setsamples = {__Pyx_NAMESTR("setsamples"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_44setsamples, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_43setsamples)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_samples = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__samples,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setsamples (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__samples,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -20239,12 +20603,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samples); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samples)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -20265,16 +20627,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setsamples", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setsamples", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_43setsamples(__pyx_self, __pyx_v_self, __pyx_v_samples); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_43setsamples(__pyx_self, __pyx_v_self, __pyx_v_samples); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":921 +/* "pysam/cvcf.pyx":921 * return self._samples * * def setsamples(self,samples): # <<<<<<<<<<<<<< @@ -20282,7 +20644,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject * self._samples = samples */ -static PyObject *__pyx_pf_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; @@ -20290,7 +20652,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setsamples", 0); - /* "cvcf.pyx":923 + /* "pysam/cvcf.pyx":923 * def setsamples(self,samples): * """ List of samples in VCF file """ * self._samples = samples # <<<<<<<<<<<<<< @@ -20302,7 +20664,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_ __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.setsamples", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setsamples", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20311,20 +20673,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_46getheader(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_45getheader[] = " List of header key-value pairs (strings) "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_46getheader = {__Pyx_NAMESTR("getheader"), (PyCFunction)__pyx_pw_4cvcf_3VCF_46getheader, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_45getheader)}; -static PyObject *__pyx_pw_4cvcf_3VCF_46getheader(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_46getheader(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_45getheader[] = " List of header key-value pairs (strings) "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_46getheader = {__Pyx_NAMESTR("getheader"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_46getheader, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_45getheader)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_46getheader(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("getheader (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_4cvcf_3VCF_45getheader(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_45getheader(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":925 +/* "pysam/cvcf.pyx":925 * self._samples = samples * * def getheader(self): # <<<<<<<<<<<<<< @@ -20332,7 +20693,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_46getheader(PyObject *__pyx_self, PyObject * return self._header */ -static PyObject *__pyx_pf_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -20341,7 +20702,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("getheader", 0); - /* "cvcf.pyx":927 + /* "pysam/cvcf.pyx":927 * def getheader(self): * """ List of header key-value pairs (strings) """ * return self._header # <<<<<<<<<<<<<< @@ -20359,7 +20720,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_s goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.getheader", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.getheader", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20368,18 +20729,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_47setheader[] = " List of header key-value pairs (strings) "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_48setheader = {__Pyx_NAMESTR("setheader"), (PyCFunction)__pyx_pw_4cvcf_3VCF_48setheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_47setheader)}; -static PyObject *__pyx_pw_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_47setheader[] = " List of header key-value pairs (strings) "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_48setheader = {__Pyx_NAMESTR("setheader"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_48setheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_47setheader)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_header = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__header,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setheader (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__header,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -20393,12 +20753,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -20419,16 +20777,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setheader", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setheader", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_47setheader(__pyx_self, __pyx_v_self, __pyx_v_header); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_47setheader(__pyx_self, __pyx_v_self, __pyx_v_header); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":929 +/* "pysam/cvcf.pyx":929 * return self._header * * def setheader(self,header): # <<<<<<<<<<<<<< @@ -20436,7 +20794,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject * self._header = header */ -static PyObject *__pyx_pf_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; @@ -20444,7 +20802,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setheader", 0); - /* "cvcf.pyx":931 + /* "pysam/cvcf.pyx":931 * def setheader(self,header): * """ List of header key-value pairs (strings) """ * self._header = header # <<<<<<<<<<<<<< @@ -20456,7 +20814,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_s __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.setheader", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setheader", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20465,20 +20823,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_50getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_49getinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_50getinfo = {__Pyx_NAMESTR("getinfo"), (PyCFunction)__pyx_pw_4cvcf_3VCF_50getinfo, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_49getinfo)}; -static PyObject *__pyx_pw_4cvcf_3VCF_50getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_50getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_49getinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_50getinfo = {__Pyx_NAMESTR("getinfo"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_50getinfo, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_49getinfo)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_50getinfo(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("getinfo (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_4cvcf_3VCF_49getinfo(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_49getinfo(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":933 +/* "pysam/cvcf.pyx":933 * self._header = header * * def getinfo(self): # <<<<<<<<<<<<<< @@ -20486,7 +20843,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_50getinfo(PyObject *__pyx_self, PyObject *_ * return self._info */ -static PyObject *__pyx_pf_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -20495,7 +20852,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_sel int __pyx_clineno = 0; __Pyx_RefNannySetupContext("getinfo", 0); - /* "cvcf.pyx":935 + /* "pysam/cvcf.pyx":935 * def getinfo(self): * """ Dictionary of ##INFO tags, as VCF.FORMAT values """ * return self._info # <<<<<<<<<<<<<< @@ -20513,7 +20870,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_sel goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.getinfo", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.getinfo", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20522,18 +20879,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_sel } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_51setinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_52setinfo = {__Pyx_NAMESTR("setinfo"), (PyCFunction)__pyx_pw_4cvcf_3VCF_52setinfo, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_51setinfo)}; -static PyObject *__pyx_pw_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_51setinfo[] = " Dictionary of ##INFO tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_52setinfo = {__Pyx_NAMESTR("setinfo"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_52setinfo, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_51setinfo)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_info = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__info,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setinfo (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__info,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -20547,12 +20903,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *_ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__info); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__info)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -20573,16 +20927,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *_ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setinfo", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setinfo", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_51setinfo(__pyx_self, __pyx_v_self, __pyx_v_info); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_51setinfo(__pyx_self, __pyx_v_self, __pyx_v_info); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":937 +/* "pysam/cvcf.pyx":937 * return self._info * * def setinfo(self,info): # <<<<<<<<<<<<<< @@ -20590,7 +20944,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *_ * self._info = info */ -static PyObject *__pyx_pf_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; @@ -20598,7 +20952,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_sel int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setinfo", 0); - /* "cvcf.pyx":939 + /* "pysam/cvcf.pyx":939 * def setinfo(self,info): * """ Dictionary of ##INFO tags, as VCF.FORMAT values """ * self._info = info # <<<<<<<<<<<<<< @@ -20610,7 +20964,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_sel __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.setinfo", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setinfo", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20619,20 +20973,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_sel } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_54getformat(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_53getformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_54getformat = {__Pyx_NAMESTR("getformat"), (PyCFunction)__pyx_pw_4cvcf_3VCF_54getformat, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_53getformat)}; -static PyObject *__pyx_pw_4cvcf_3VCF_54getformat(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_54getformat(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_53getformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_54getformat = {__Pyx_NAMESTR("getformat"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_54getformat, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_53getformat)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_54getformat(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("getformat (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_4cvcf_3VCF_53getformat(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_53getformat(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":941 +/* "pysam/cvcf.pyx":941 * self._info = info * * def getformat(self): # <<<<<<<<<<<<<< @@ -20640,7 +20993,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_54getformat(PyObject *__pyx_self, PyObject * return self._format */ -static PyObject *__pyx_pf_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -20649,7 +21002,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("getformat", 0); - /* "cvcf.pyx":943 + /* "pysam/cvcf.pyx":943 * def getformat(self): * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * return self._format # <<<<<<<<<<<<<< @@ -20667,7 +21020,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_s goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.getformat", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.getformat", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20676,18 +21029,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_55setformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_56setformat = {__Pyx_NAMESTR("setformat"), (PyCFunction)__pyx_pw_4cvcf_3VCF_56setformat, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_55setformat)}; -static PyObject *__pyx_pw_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_55setformat[] = " Dictionary of ##FORMAT tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_56setformat = {__Pyx_NAMESTR("setformat"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_56setformat, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_55setformat)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_format = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setformat (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -20701,12 +21053,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -20727,16 +21077,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setformat", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setformat", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_55setformat(__pyx_self, __pyx_v_self, __pyx_v_format); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_55setformat(__pyx_self, __pyx_v_self, __pyx_v_format); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":945 +/* "pysam/cvcf.pyx":945 * return self._format * * def setformat(self,format): # <<<<<<<<<<<<<< @@ -20744,7 +21094,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject * self._format = format */ -static PyObject *__pyx_pf_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; @@ -20752,7 +21102,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setformat", 0); - /* "cvcf.pyx":947 + /* "pysam/cvcf.pyx":947 * def setformat(self,format): * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * self._format = format # <<<<<<<<<<<<<< @@ -20764,7 +21114,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_s __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.setformat", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setformat", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20773,20 +21123,19 @@ static PyObject *__pyx_pf_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_58getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_57getfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_58getfilter = {__Pyx_NAMESTR("getfilter"), (PyCFunction)__pyx_pw_4cvcf_3VCF_58getfilter, METH_O, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_57getfilter)}; -static PyObject *__pyx_pw_4cvcf_3VCF_58getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_58getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_57getfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_58getfilter = {__Pyx_NAMESTR("getfilter"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_58getfilter, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_57getfilter)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_58getfilter(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("getfilter (wrapper)", 0); - __pyx_self = __pyx_self; - __pyx_r = __pyx_pf_4cvcf_3VCF_57getfilter(__pyx_self, ((PyObject *)__pyx_v_self)); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_57getfilter(__pyx_self, ((PyObject *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":949 +/* "pysam/cvcf.pyx":949 * self._format = format * * def getfilter(self): # <<<<<<<<<<<<<< @@ -20794,7 +21143,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_58getfilter(PyObject *__pyx_self, PyObject * return self._filter */ -static PyObject *__pyx_pf_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -20803,7 +21152,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("getfilter", 0); - /* "cvcf.pyx":951 + /* "pysam/cvcf.pyx":951 * def getfilter(self): * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * return self._filter # <<<<<<<<<<<<<< @@ -20821,7 +21170,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_s goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.getfilter", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.getfilter", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20830,18 +21179,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_59setfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_60setfilter = {__Pyx_NAMESTR("setfilter"), (PyCFunction)__pyx_pw_4cvcf_3VCF_60setfilter, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_59setfilter)}; -static PyObject *__pyx_pw_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_59setfilter[] = " Dictionary of ##FILTER tags, as VCF.FORMAT values "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_60setfilter = {__Pyx_NAMESTR("setfilter"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_60setfilter, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_59setfilter)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_filter = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filter,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setfilter (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filter,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -20855,12 +21203,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filter); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filter)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -20881,16 +21227,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setfilter", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setfilter", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_59setfilter(__pyx_self, __pyx_v_self, __pyx_v_filter); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_59setfilter(__pyx_self, __pyx_v_self, __pyx_v_filter); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":953 +/* "pysam/cvcf.pyx":953 * return self._filter * * def setfilter(self,filter): # <<<<<<<<<<<<<< @@ -20898,7 +21244,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject * self._filter = filter */ -static PyObject *__pyx_pf_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; @@ -20906,7 +21252,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setfilter", 0); - /* "cvcf.pyx":955 + /* "pysam/cvcf.pyx":955 * def setfilter(self,filter): * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * self._filter = filter # <<<<<<<<<<<<<< @@ -20918,7 +21264,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_s __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.setfilter", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setfilter", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -20927,17 +21273,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_62setversion = {__Pyx_NAMESTR("setversion"), (PyCFunction)__pyx_pw_4cvcf_3VCF_62setversion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_62setversion = {__Pyx_NAMESTR("setversion"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_62setversion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_version = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setversion (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -20951,12 +21296,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__version); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__version)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -20977,16 +21320,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setversion", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setversion", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_61setversion(__pyx_self, __pyx_v_self, __pyx_v_version); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_61setversion(__pyx_self, __pyx_v_self, __pyx_v_version); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":957 +/* "pysam/cvcf.pyx":957 * self._filter = filter * * def setversion(self, version): # <<<<<<<<<<<<<< @@ -20994,7 +21337,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject * self._version = version */ -static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -21006,20 +21349,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setversion", 0); - /* "cvcf.pyx":958 + /* "pysam/cvcf.pyx":958 * * def setversion(self, version): * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") # <<<<<<<<<<<<<< * self._version = version * */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_33, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_33, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { - __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_40, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_40, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_4 = __pyx_t_3; @@ -21036,7 +21377,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_ } __pyx_L3:; - /* "cvcf.pyx":959 + /* "pysam/cvcf.pyx":959 * def setversion(self, version): * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") * self._version = version # <<<<<<<<<<<<<< @@ -21049,7 +21390,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.setversion", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setversion", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -21058,17 +21399,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_64setregions = {__Pyx_NAMESTR("setregions"), (PyCFunction)__pyx_pw_4cvcf_3VCF_64setregions, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_64setregions = {__Pyx_NAMESTR("setregions"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_64setregions, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_regions = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__regions,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setregions (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__regions,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -21082,12 +21422,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__regions); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__regions)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -21108,16 +21446,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setregions", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setregions", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_63setregions(__pyx_self, __pyx_v_self, __pyx_v_regions); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_63setregions(__pyx_self, __pyx_v_self, __pyx_v_regions); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":961 +/* "pysam/cvcf.pyx":961 * self._version = version * * def setregions(self, regions): # <<<<<<<<<<<<<< @@ -21125,7 +21463,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject * */ -static PyObject *__pyx_pf_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; @@ -21133,7 +21471,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setregions", 0); - /* "cvcf.pyx":962 + /* "pysam/cvcf.pyx":962 * * def setregions(self, regions): * self._regions = regions # <<<<<<<<<<<<<< @@ -21145,7 +21483,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_ __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.setregions", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setregions", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -21154,18 +21492,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_ } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_65setreference[] = " Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_66setreference = {__Pyx_NAMESTR("setreference"), (PyCFunction)__pyx_pw_4cvcf_3VCF_66setreference, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_65setreference)}; -static PyObject *__pyx_pw_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_65setreference[] = " Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_66setreference = {__Pyx_NAMESTR("setreference"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_66setreference, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_65setreference)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_ref = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__ref,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("setreference (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__ref,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -21179,12 +21516,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObje kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -21205,16 +21540,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObje __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.setreference", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setreference", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_65setreference(__pyx_self, __pyx_v_self, __pyx_v_ref); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_65setreference(__pyx_self, __pyx_v_self, __pyx_v_ref); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":964 +/* "pysam/cvcf.pyx":964 * self._regions = regions * * def setreference(self, ref): # <<<<<<<<<<<<<< @@ -21222,7 +21557,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObje * self._reference = ref */ -static PyObject *__pyx_pf_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_lineno = 0; @@ -21230,7 +21565,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__py int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setreference", 0); - /* "cvcf.pyx":966 + /* "pysam/cvcf.pyx":966 * def setreference(self, ref): * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """ * self._reference = ref # <<<<<<<<<<<<<< @@ -21242,7 +21577,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__py __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; - __Pyx_AddTraceback("cvcf.VCF.setreference", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.setreference", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -21251,17 +21586,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__py } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_68ignoreerror = {__Pyx_NAMESTR("ignoreerror"), (PyCFunction)__pyx_pw_4cvcf_3VCF_68ignoreerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_68ignoreerror = {__Pyx_NAMESTR("ignoreerror"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_errorstring = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("ignoreerror (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -21275,12 +21609,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObjec kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -21301,16 +21633,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObjec __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_67ignoreerror(__pyx_self, __pyx_v_self, __pyx_v_errorstring); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(__pyx_self, __pyx_v_self, __pyx_v_errorstring); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":968 +/* "pysam/cvcf.pyx":968 * self._reference = ref * * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<< @@ -21318,7 +21650,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObjec * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ -static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -21335,7 +21667,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx int __pyx_clineno = 0; __Pyx_RefNannySetupContext("ignoreerror", 0); - /* "cvcf.pyx":969 + /* "pysam/cvcf.pyx":969 * * def ignoreerror(self, errorstring): * try: self._ignored_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<< @@ -21378,7 +21710,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "cvcf.pyx":970 + /* "pysam/cvcf.pyx":970 * def ignoreerror(self, errorstring): * try: self._ignored_errors.add(self.__dict__[errorstring]) * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) # <<<<<<<<<<<<<< @@ -21387,7 +21719,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx */ __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_KeyError); if (__pyx_t_7) { - __Pyx_AddTraceback("cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_4, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_4); @@ -21432,7 +21764,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_8); __Pyx_XDECREF(__pyx_t_9); - __Pyx_AddTraceback("cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -21441,17 +21773,16 @@ static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef __pyx_mdef_4cvcf_3VCF_70warnerror = {__Pyx_NAMESTR("warnerror"), (PyCFunction)__pyx_pw_4cvcf_3VCF_70warnerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; -static PyObject *__pyx_pw_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_70warnerror = {__Pyx_NAMESTR("warnerror"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_70warnerror, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_errorstring = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("warnerror (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -21465,12 +21796,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -21491,16 +21820,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_69warnerror(__pyx_self, __pyx_v_self, __pyx_v_errorstring); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_69warnerror(__pyx_self, __pyx_v_self, __pyx_v_errorstring); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":972 +/* "pysam/cvcf.pyx":972 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) * * def warnerror(self, errorstring): # <<<<<<<<<<<<<< @@ -21508,7 +21837,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ -static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -21525,7 +21854,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_s int __pyx_clineno = 0; __Pyx_RefNannySetupContext("warnerror", 0); - /* "cvcf.pyx":973 + /* "pysam/cvcf.pyx":973 * * def warnerror(self, errorstring): * try: self._warn_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<< @@ -21568,7 +21897,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_s __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; - /* "cvcf.pyx":974 + /* "pysam/cvcf.pyx":974 * def warnerror(self, errorstring): * try: self._warn_errors.add(self.__dict__[errorstring]) * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) # <<<<<<<<<<<<<< @@ -21577,7 +21906,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_s */ __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_KeyError); if (__pyx_t_7) { - __Pyx_AddTraceback("cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename); if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_4, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 974; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_GOTREF(__pyx_t_4); @@ -21622,7 +21951,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_s __Pyx_XDECREF(__pyx_t_6); __Pyx_XDECREF(__pyx_t_8); __Pyx_XDECREF(__pyx_t_9); - __Pyx_AddTraceback("cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -21631,18 +21960,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_s } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_71parse[] = " Parse a stream of VCF-formatted lines. Initializes class instance and return generator "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_72parse = {__Pyx_NAMESTR("parse"), (PyCFunction)__pyx_pw_4cvcf_3VCF_72parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_71parse)}; -static PyObject *__pyx_pw_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_71parse[] = " Parse a stream of VCF-formatted lines. Initializes class instance and return generator "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_72parse = {__Pyx_NAMESTR("parse"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_72parse, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_71parse)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("parse (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -21656,12 +21984,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__p kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -21682,16 +22008,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__p __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_71parse(__pyx_self, __pyx_v_self, __pyx_v_stream); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_71parse(__pyx_self, __pyx_v_self, __pyx_v_stream); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":976 +/* "pysam/cvcf.pyx":976 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) * * def parse(self, stream): # <<<<<<<<<<<<<< @@ -21699,7 +22025,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__p * last_line = self._parse_header(stream) */ -static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { PyObject *__pyx_v_last_line = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -21711,7 +22037,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_clineno = 0; __Pyx_RefNannySetupContext("parse", 0); - /* "cvcf.pyx":978 + /* "pysam/cvcf.pyx":978 * def parse(self, stream): * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ * last_line = self._parse_header(stream) # <<<<<<<<<<<<<< @@ -21732,7 +22058,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, __pyx_v_last_line = __pyx_t_3; __pyx_t_3 = 0; - /* "cvcf.pyx":981 + /* "pysam/cvcf.pyx":981 * # now return a generator that does the actual work. In this way the pre-processing is done * # before the first piece of data is yielded * return self._parse(last_line, stream) # <<<<<<<<<<<<<< @@ -21764,7 +22090,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("cvcf.VCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_last_line); @@ -21774,19 +22100,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_73write[] = " Writes a VCF file to a stream, using a data generator (or list) "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_74write = {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_4cvcf_3VCF_74write, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_73write)}; -static PyObject *__pyx_pw_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_73write[] = " Writes a VCF file to a stream, using a data generator (or list) "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_74write = {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_74write, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_73write)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; PyObject *__pyx_v_datagenerator = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__datagenerator,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("write (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__datagenerator,0}; PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -21801,18 +22126,15 @@ static PyObject *__pyx_pw_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObject *__p kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__datagenerator); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__datagenerator)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -21835,16 +22157,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObject *__p __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.write", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.write", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_73write(__pyx_self, __pyx_v_self, __pyx_v_stream, __pyx_v_datagenerator); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_73write(__pyx_self, __pyx_v_self, __pyx_v_stream, __pyx_v_datagenerator); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":983 +/* "pysam/cvcf.pyx":983 * return self._parse(last_line, stream) * * def write(self, stream, datagenerator): # <<<<<<<<<<<<<< @@ -21852,7 +22174,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObject *__p * self.write_header(stream) */ -static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator) { PyObject *__pyx_v_data = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -21867,7 +22189,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_clineno = 0; __Pyx_RefNannySetupContext("write", 0); - /* "cvcf.pyx":985 + /* "pysam/cvcf.pyx":985 * def write(self, stream, datagenerator): * """ Writes a VCF file to a stream, using a data generator (or list) """ * self.write_header(stream) # <<<<<<<<<<<<<< @@ -21887,7 +22209,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":986 + /* "pysam/cvcf.pyx":986 * """ Writes a VCF file to a stream, using a data generator (or list) """ * self.write_header(stream) * self.write_heading(stream) # <<<<<<<<<<<<<< @@ -21907,7 +22229,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":987 + /* "pysam/cvcf.pyx":987 * self.write_header(stream) * self.write_heading(stream) * for data in datagenerator: self.write_data(stream,data) # <<<<<<<<<<<<<< @@ -21925,10 +22247,18 @@ static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, for (;;) { if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break; - __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; + #if CYTHON_COMPILING_IN_CPYTHON + __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #else + __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif } else { __pyx_t_2 = __pyx_t_5(__pyx_t_1); if (unlikely(!__pyx_t_2)) { @@ -21968,7 +22298,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("cvcf.VCF.write", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.write", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_data); @@ -21978,18 +22308,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_75writeheader[] = " Writes a VCF header "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_76writeheader = {__Pyx_NAMESTR("writeheader"), (PyCFunction)__pyx_pw_4cvcf_3VCF_76writeheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_75writeheader)}; -static PyObject *__pyx_pw_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_75writeheader[] = " Writes a VCF header "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_76writeheader = {__Pyx_NAMESTR("writeheader"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_76writeheader, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_75writeheader)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_stream = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("writeheader (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -22003,12 +22332,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObjec kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -22029,16 +22356,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObjec __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.writeheader", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.writeheader", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_75writeheader(__pyx_self, __pyx_v_self, __pyx_v_stream); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_75writeheader(__pyx_self, __pyx_v_self, __pyx_v_stream); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":989 +/* "pysam/cvcf.pyx":989 * for data in datagenerator: self.write_data(stream,data) * * def writeheader(self, stream): # <<<<<<<<<<<<<< @@ -22046,7 +22373,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObjec * self.write_header(stream) */ -static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -22057,7 +22384,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx int __pyx_clineno = 0; __Pyx_RefNannySetupContext("writeheader", 0); - /* "cvcf.pyx":991 + /* "pysam/cvcf.pyx":991 * def writeheader(self, stream): * """ Writes a VCF header """ * self.write_header(stream) # <<<<<<<<<<<<<< @@ -22077,7 +22404,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":992 + /* "pysam/cvcf.pyx":992 * """ Writes a VCF header """ * self.write_header(stream) * self.write_heading(stream) # <<<<<<<<<<<<<< @@ -22103,7 +22430,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("cvcf.VCF.writeheader", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.writeheader", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -22112,10 +22439,10 @@ static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_77compare_calls[] = " Utility function: compares two calls for equality "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_78compare_calls = {__Pyx_NAMESTR("compare_calls"), (PyCFunction)__pyx_pw_4cvcf_3VCF_78compare_calls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_77compare_calls)}; -static PyObject *__pyx_pw_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_77compare_calls[] = " Utility function: compares two calls for equality "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_78compare_calls = {__Pyx_NAMESTR("compare_calls"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_78compare_calls, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_77compare_calls)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { CYTHON_UNUSED PyObject *__pyx_v_self = 0; PyObject *__pyx_v_pos1 = 0; PyObject *__pyx_v_ref1 = 0; @@ -22123,12 +22450,11 @@ static PyObject *__pyx_pw_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObj PyObject *__pyx_v_pos2 = 0; PyObject *__pyx_v_ref2 = 0; PyObject *__pyx_v_alt2 = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__pos1,&__pyx_n_s__ref1,&__pyx_n_s__alt1,&__pyx_n_s__pos2,&__pyx_n_s__ref2,&__pyx_n_s__alt2,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("compare_calls (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__pos1,&__pyx_n_s__ref1,&__pyx_n_s__alt1,&__pyx_n_s__pos2,&__pyx_n_s__ref2,&__pyx_n_s__alt2,0}; PyObject* values[7] = {0,0,0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -22147,42 +22473,35 @@ static PyObject *__pyx_pw_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObj kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos1); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos1)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref1); - if (likely(values[2])) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref1)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: - values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt1); - if (likely(values[3])) kw_args--; + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt1)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: - values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos2); - if (likely(values[4])) kw_args--; + if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos2)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: - values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref2); - if (likely(values[5])) kw_args--; + if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref2)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 6: - values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2); - if (likely(values[6])) kw_args--; + if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -22213,16 +22532,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObj __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.compare_calls", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.compare_calls", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_77compare_calls(__pyx_self, __pyx_v_self, __pyx_v_pos1, __pyx_v_ref1, __pyx_v_alt1, __pyx_v_pos2, __pyx_v_ref2, __pyx_v_alt2); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(__pyx_self, __pyx_v_self, __pyx_v_pos1, __pyx_v_ref1, __pyx_v_alt1, __pyx_v_pos2, __pyx_v_ref2, __pyx_v_alt2); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":994 +/* "pysam/cvcf.pyx":994 * self.write_heading(stream) * * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<< @@ -22230,7 +22549,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self, PyObj * # a variant should always be assigned to a unique position, one base before */ -static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -22250,15 +22569,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __Pyx_INCREF(__pyx_v_ref2); __Pyx_INCREF(__pyx_v_alt2); - /* "cvcf.pyx":999 + /* "pysam/cvcf.pyx":999 * # the leftmost position of the alignment gap. If this rule is implemented * # correctly, the two positions must be equal for the calls to be identical. * if pos1 != pos2: return False # <<<<<<<<<<<<<< * # from both calls, trim rightmost bases when identical. Do this safely, i.e. * # only when the reference bases are not Ns */ - __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (__pyx_t_2) { @@ -22272,7 +22590,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p } __pyx_L3:; - /* "cvcf.pyx":1002 + /* "pysam/cvcf.pyx":1002 * # from both calls, trim rightmost bases when identical. Do this safely, i.e. * # only when the reference bases are not Ns * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: # <<<<<<<<<<<<<< @@ -22290,8 +22608,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __Pyx_GOTREF(__pyx_t_1); __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -22306,7 +22623,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p } if (!__pyx_t_4) break; - /* "cvcf.pyx":1003 + /* "pysam/cvcf.pyx":1003 * # only when the reference bases are not Ns * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: * ref1 = ref1[:-1] # <<<<<<<<<<<<<< @@ -22319,7 +22636,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __pyx_v_ref1 = __pyx_t_6; __pyx_t_6 = 0; - /* "cvcf.pyx":1004 + /* "pysam/cvcf.pyx":1004 * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: * ref1 = ref1[:-1] * alt1 = alt1[:-1] # <<<<<<<<<<<<<< @@ -22333,7 +22650,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __pyx_t_6 = 0; } - /* "cvcf.pyx":1005 + /* "pysam/cvcf.pyx":1005 * ref1 = ref1[:-1] * alt1 = alt1[:-1] * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: # <<<<<<<<<<<<<< @@ -22351,8 +22668,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __Pyx_GOTREF(__pyx_t_6); __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt2, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -22367,7 +22683,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p } if (!__pyx_t_2) break; - /* "cvcf.pyx":1006 + /* "pysam/cvcf.pyx":1006 * alt1 = alt1[:-1] * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: * ref2 = ref2[:-1] # <<<<<<<<<<<<<< @@ -22380,7 +22696,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __pyx_v_ref2 = __pyx_t_1; __pyx_t_1 = 0; - /* "cvcf.pyx":1007 + /* "pysam/cvcf.pyx":1007 * while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: * ref2 = ref2[:-1] * alt2 = alt2[:-1] # <<<<<<<<<<<<<< @@ -22394,7 +22710,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __pyx_t_1 = 0; } - /* "cvcf.pyx":1009 + /* "pysam/cvcf.pyx":1009 * alt2 = alt2[:-1] * # now, the alternative alleles must be identical * return alt1 == alt2 # <<<<<<<<<<<<<< @@ -22402,8 +22718,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p * ########################################################################################################### */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; @@ -22414,7 +22729,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_5); __Pyx_XDECREF(__pyx_t_6); - __Pyx_AddTraceback("cvcf.VCF.compare_calls", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.compare_calls", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF(__pyx_v_ref1); @@ -22427,18 +22742,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__p } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_79connect[] = "connect to tabix file."; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_80connect = {__Pyx_NAMESTR("connect"), (PyCFunction)__pyx_pw_4cvcf_3VCF_80connect, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_79connect)}; -static PyObject *__pyx_pw_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_79connect[] = "connect to tabix file."; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_80connect = {__Pyx_NAMESTR("connect"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_80connect, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_79connect)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_filename = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("connect (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -22452,12 +22766,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *_ kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -22478,16 +22790,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *_ __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.connect", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.connect", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_79connect(__pyx_self, __pyx_v_self, __pyx_v_filename); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_79connect(__pyx_self, __pyx_v_self, __pyx_v_filename); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":1016 +/* "pysam/cvcf.pyx":1016 * ########################################################################################################### * * def connect( self, filename ): # <<<<<<<<<<<<<< @@ -22495,7 +22807,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *_ * self.tabixfile = pysam.Tabixfile( filename ) */ -static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -22506,7 +22818,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_sel int __pyx_clineno = 0; __Pyx_RefNannySetupContext("connect", 0); - /* "cvcf.pyx":1018 + /* "pysam/cvcf.pyx":1018 * def connect( self, filename ): * '''connect to tabix file.''' * self.tabixfile = pysam.Tabixfile( filename ) # <<<<<<<<<<<<<< @@ -22530,7 +22842,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_sel if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__tabixfile, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "cvcf.pyx":1019 + /* "pysam/cvcf.pyx":1019 * '''connect to tabix file.''' * self.tabixfile = pysam.Tabixfile( filename ) * self._parse_header(self.tabixfile.header) # <<<<<<<<<<<<<< @@ -22561,7 +22873,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); - __Pyx_AddTraceback("cvcf.VCF.connect", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.connect", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -22570,24 +22882,23 @@ static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_sel } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_81fetch[] = " Parse a stream of VCF-formatted lines. Initializes class instance and return generator "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_82fetch = {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_4cvcf_3VCF_82fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_81fetch)}; -static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_81fetch[] = " Parse a stream of VCF-formatted lines. Initializes class instance and return generator "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_82fetch = {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_82fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_81fetch)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_region = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("fetch (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0}; PyObject* values[5] = {0,0,0,0,0}; - /* "cvcf.pyx":1022 + /* "pysam/cvcf.pyx":1022 * * def fetch(self, * reference = None, # <<<<<<<<<<<<<< @@ -22596,7 +22907,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__p */ values[1] = ((PyObject *)((PyObject *)Py_None)); - /* "cvcf.pyx":1023 + /* "pysam/cvcf.pyx":1023 * def fetch(self, * reference = None, * start = None, # <<<<<<<<<<<<<< @@ -22605,7 +22916,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__p */ values[2] = ((PyObject *)((PyObject *)Py_None)); - /* "cvcf.pyx":1024 + /* "pysam/cvcf.pyx":1024 * reference = None, * start = None, * end = None, # <<<<<<<<<<<<<< @@ -22614,7 +22925,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__p */ values[3] = ((PyObject *)((PyObject *)Py_None)); - /* "cvcf.pyx":1025 + /* "pysam/cvcf.pyx":1025 * start = None, * end = None, * region = None ): # <<<<<<<<<<<<<< @@ -22637,8 +22948,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__p kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (kw_args > 0) { @@ -22685,16 +22995,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__p __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("fetch", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_81fetch(__pyx_self, __pyx_v_self, __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_81fetch(__pyx_self, __pyx_v_self, __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":1021 +/* "pysam/cvcf.pyx":1021 * self._parse_header(self.tabixfile.header) * * def fetch(self, # <<<<<<<<<<<<<< @@ -22702,7 +23012,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObject *__p * start = None, */ -static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -22715,7 +23025,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_clineno = 0; __Pyx_RefNannySetupContext("fetch", 0); - /* "cvcf.pyx":1028 + /* "pysam/cvcf.pyx":1028 * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ * * return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) ) # <<<<<<<<<<<<<< @@ -22749,7 +23059,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_INCREF(__pyx_v_self); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_self); __Pyx_GIVEREF(__pyx_v_self); - __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_4cvcf_asVCFRecord)), ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_4cvcf_asVCFRecord)), ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__parser), __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -22771,7 +23081,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); - __Pyx_AddTraceback("cvcf.VCF.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); @@ -22780,18 +23090,17 @@ static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, } /* Python wrapper */ -static PyObject *__pyx_pw_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_4cvcf_3VCF_83validate[] = "validate vcf record.\n\n returns a validated record.\n "; -static PyMethodDef __pyx_mdef_4cvcf_3VCF_84validate = {__Pyx_NAMESTR("validate"), (PyCFunction)__pyx_pw_4cvcf_3VCF_84validate, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_3VCF_83validate)}; -static PyObject *__pyx_pw_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_5pysam_4cvcf_3VCF_83validate[] = "validate vcf record.\n\n returns a validated record.\n "; +static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_84validate = {__Pyx_NAMESTR("validate"), (PyCFunction)__pyx_pw_5pysam_4cvcf_3VCF_84validate, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_3VCF_83validate)}; +static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { CYTHON_UNUSED PyObject *__pyx_v_self = 0; CYTHON_UNUSED PyObject *__pyx_v_record = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0}; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("validate (wrapper)", 0); - __pyx_self = __pyx_self; { + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; @@ -22805,12 +23114,10 @@ static PyObject *__pyx_pw_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject * kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: - values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self); - if (likely(values[0])) kw_args--; + if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record); - if (likely(values[1])) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } @@ -22831,16 +23138,16 @@ static PyObject *__pyx_pw_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject * __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; - __Pyx_AddTraceback("cvcf.VCF.validate", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.validate", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_4cvcf_3VCF_83validate(__pyx_self, __pyx_v_self, __pyx_v_record); + __pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_83validate(__pyx_self, __pyx_v_self, __pyx_v_record); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "cvcf.pyx":1030 +/* "pysam/cvcf.pyx":1030 * return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) ) * * def validate( self, record ): # <<<<<<<<<<<<<< @@ -22848,7 +23155,7 @@ static PyObject *__pyx_pw_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject * * */ -static PyObject *__pyx_pf_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record) { +static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -22857,7 +23164,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_se int __pyx_clineno = 0; __Pyx_RefNannySetupContext("validate", 0); - /* "cvcf.pyx":1036 + /* "pysam/cvcf.pyx":1036 * ''' * * raise NotImplementedError( "needs to be checked" ) # <<<<<<<<<<<<<< @@ -22874,58 +23181,56 @@ static PyObject *__pyx_pf_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_se goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); - __Pyx_AddTraceback("cvcf.VCF.validate", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("pysam.cvcf.VCF.validate", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } -static struct __pyx_vtabstruct_4cvcf_VCFRecord __pyx_vtable_4cvcf_VCFRecord; +static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord __pyx_vtable_5pysam_4cvcf_VCFRecord; -static PyObject *__pyx_tp_new_4cvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_4cvcf_VCFRecord *p; - PyObject *o = __pyx_ptype_10TabProxies_TupleProxy->tp_new(t, a, k); +static PyObject *__pyx_tp_new_5pysam_4cvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_5pysam_4cvcf_VCFRecord *p; + PyObject *o = __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_new(t, a, k); if (!o) return 0; - p = ((struct __pyx_obj_4cvcf_VCFRecord *)o); - p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_4cvcf_VCFRecord; + p = ((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_4cvcf_VCFRecord; p->vcf = Py_None; Py_INCREF(Py_None); - if (__pyx_pw_4cvcf_9VCFRecord_3__cinit__(o, a, k) < 0) { + if (__pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } -static void __pyx_tp_dealloc_4cvcf_VCFRecord(PyObject *o) { - struct __pyx_obj_4cvcf_VCFRecord *p = (struct __pyx_obj_4cvcf_VCFRecord *)o; - Py_XDECREF(p->vcf); - __pyx_ptype_10TabProxies_TupleProxy->tp_dealloc(o); +static void __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; + PyObject_GC_UnTrack(o); + Py_CLEAR(p->vcf); + PyObject_GC_Track(o); + if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord); } -static int __pyx_tp_traverse_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_4cvcf_VCFRecord *p = (struct __pyx_obj_4cvcf_VCFRecord *)o; - if (__pyx_ptype_10TabProxies_TupleProxy->tp_traverse) { - e = __pyx_ptype_10TabProxies_TupleProxy->tp_traverse(o, v, a); if (e) return e; - } + struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; + e = ((likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) ? ((__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) ? __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_VCFRecord)); if (e) return e; if (p->vcf) { e = (*v)(p->vcf, a); if (e) return e; } return 0; } -static int __pyx_tp_clear_4cvcf_VCFRecord(PyObject *o) { - struct __pyx_obj_4cvcf_VCFRecord *p = (struct __pyx_obj_4cvcf_VCFRecord *)o; +static int __pyx_tp_clear_5pysam_4cvcf_VCFRecord(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; PyObject* tmp; - if (__pyx_ptype_10TabProxies_TupleProxy->tp_clear) { - __pyx_ptype_10TabProxies_TupleProxy->tp_clear(o); - } + if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) { if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_VCFRecord); tmp = ((PyObject*)p->vcf); p->vcf = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } -static PyObject *__pyx_sq_item_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i) { +static PyObject *__pyx_sq_item_5pysam_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i) { PyObject *r; PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); @@ -22933,62 +23238,62 @@ static PyObject *__pyx_sq_item_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i) { return r; } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_contig(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_6contig_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_pos(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_3pos_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_id(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_2id_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_ref(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_3ref_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_alt(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_3alt_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_qual(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_4qual_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_filter(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_6filter_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_info(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_4info_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_format(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_6format_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(o); } -static PyObject *__pyx_getprop_4cvcf_9VCFRecord_samples(PyObject *o, void *x) { - return __pyx_pw_4cvcf_9VCFRecord_7samples_1__get__(o); +static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(o); } -static PyMethodDef __pyx_methods_4cvcf_VCFRecord[] = { - {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_4cvcf_9VCFRecord_5error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_9VCFRecord_4error)}, +static PyMethodDef __pyx_methods_5pysam_4cvcf_VCFRecord[] = { + {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_5pysam_4cvcf_9VCFRecord_5error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_9VCFRecord_4error)}, {0, 0, 0, 0} }; -static struct PyGetSetDef __pyx_getsets_4cvcf_VCFRecord[] = { - {(char *)"contig", __pyx_getprop_4cvcf_9VCFRecord_contig, 0, 0, 0}, - {(char *)"pos", __pyx_getprop_4cvcf_9VCFRecord_pos, 0, 0, 0}, - {(char *)"id", __pyx_getprop_4cvcf_9VCFRecord_id, 0, 0, 0}, - {(char *)"ref", __pyx_getprop_4cvcf_9VCFRecord_ref, 0, 0, 0}, - {(char *)"alt", __pyx_getprop_4cvcf_9VCFRecord_alt, 0, 0, 0}, - {(char *)"qual", __pyx_getprop_4cvcf_9VCFRecord_qual, 0, 0, 0}, - {(char *)"filter", __pyx_getprop_4cvcf_9VCFRecord_filter, 0, 0, 0}, - {(char *)"info", __pyx_getprop_4cvcf_9VCFRecord_info, 0, 0, 0}, - {(char *)"format", __pyx_getprop_4cvcf_9VCFRecord_format, 0, 0, 0}, - {(char *)"samples", __pyx_getprop_4cvcf_9VCFRecord_samples, 0, 0, 0}, +static struct PyGetSetDef __pyx_getsets_5pysam_4cvcf_VCFRecord[] = { + {(char *)"contig", __pyx_getprop_5pysam_4cvcf_9VCFRecord_contig, 0, 0, 0}, + {(char *)"pos", __pyx_getprop_5pysam_4cvcf_9VCFRecord_pos, 0, 0, 0}, + {(char *)"id", __pyx_getprop_5pysam_4cvcf_9VCFRecord_id, 0, 0, 0}, + {(char *)"ref", __pyx_getprop_5pysam_4cvcf_9VCFRecord_ref, 0, 0, 0}, + {(char *)"alt", __pyx_getprop_5pysam_4cvcf_9VCFRecord_alt, 0, 0, 0}, + {(char *)"qual", __pyx_getprop_5pysam_4cvcf_9VCFRecord_qual, 0, 0, 0}, + {(char *)"filter", __pyx_getprop_5pysam_4cvcf_9VCFRecord_filter, 0, 0, 0}, + {(char *)"info", __pyx_getprop_5pysam_4cvcf_9VCFRecord_info, 0, 0, 0}, + {(char *)"format", __pyx_getprop_5pysam_4cvcf_9VCFRecord_format, 0, 0, 0}, + {(char *)"samples", __pyx_getprop_5pysam_4cvcf_9VCFRecord_samples, 0, 0, 0}, {0, 0, 0, 0, 0} }; @@ -23051,10 +23356,10 @@ static PyNumberMethods __pyx_tp_as_number_VCFRecord = { }; static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = { - __pyx_pw_4cvcf_9VCFRecord_7__len__, /*sq_length*/ + __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ - __pyx_sq_item_4cvcf_VCFRecord, /*sq_item*/ + __pyx_sq_item_5pysam_4cvcf_VCFRecord, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ @@ -23064,8 +23369,8 @@ static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = { }; static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = { - __pyx_pw_4cvcf_9VCFRecord_7__len__, /*mp_length*/ - __pyx_pw_4cvcf_9VCFRecord_9__getitem__, /*mp_subscript*/ + __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*mp_length*/ + __pyx_pw_5pysam_4cvcf_9VCFRecord_9__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; @@ -23090,12 +23395,12 @@ static PyBufferProcs __pyx_tp_as_buffer_VCFRecord = { #endif }; -static PyTypeObject __pyx_type_4cvcf_VCFRecord = { +static PyTypeObject __pyx_type_5pysam_4cvcf_VCFRecord = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("cvcf.VCFRecord"), /*tp_name*/ - sizeof(struct __pyx_obj_4cvcf_VCFRecord), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.cvcf.VCFRecord"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_4cvcf_VCFRecord), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_4cvcf_VCFRecord, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -23116,23 +23421,23 @@ static PyTypeObject __pyx_type_4cvcf_VCFRecord = { &__pyx_tp_as_buffer_VCFRecord, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("vcf record.\n\n initialized from data and vcf meta \n "), /*tp_doc*/ - __pyx_tp_traverse_4cvcf_VCFRecord, /*tp_traverse*/ - __pyx_tp_clear_4cvcf_VCFRecord, /*tp_clear*/ + __pyx_tp_traverse_5pysam_4cvcf_VCFRecord, /*tp_traverse*/ + __pyx_tp_clear_5pysam_4cvcf_VCFRecord, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_4cvcf_VCFRecord, /*tp_methods*/ + __pyx_methods_5pysam_4cvcf_VCFRecord, /*tp_methods*/ 0, /*tp_members*/ - __pyx_getsets_4cvcf_VCFRecord, /*tp_getset*/ + __pyx_getsets_5pysam_4cvcf_VCFRecord, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_4cvcf_9VCFRecord_1__init__, /*tp_init*/ + __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_4cvcf_VCFRecord, /*tp_new*/ + __pyx_tp_new_5pysam_4cvcf_VCFRecord, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -23146,46 +23451,44 @@ static PyTypeObject __pyx_type_4cvcf_VCFRecord = { #endif }; -static PyObject *__pyx_tp_new_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_4cvcf_asVCFRecord *p; - PyObject *o = __pyx_ptype_6ctabix_Parser->tp_new(t, a, k); +static PyObject *__pyx_tp_new_5pysam_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p; + PyObject *o = __pyx_ptype_5pysam_6ctabix_Parser->tp_new(t, a, k); if (!o) return 0; - p = ((struct __pyx_obj_4cvcf_asVCFRecord *)o); + p = ((struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o); p->vcffile = Py_None; Py_INCREF(Py_None); return o; } -static void __pyx_tp_dealloc_4cvcf_asVCFRecord(PyObject *o) { - struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o; - Py_XDECREF(p->vcffile); - __pyx_ptype_6ctabix_Parser->tp_dealloc(o); +static void __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; + PyObject_GC_UnTrack(o); + Py_CLEAR(p->vcffile); + PyObject_GC_Track(o); + if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord); } -static int __pyx_tp_traverse_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o; - if (__pyx_ptype_6ctabix_Parser->tp_traverse) { - e = __pyx_ptype_6ctabix_Parser->tp_traverse(o, v, a); if (e) return e; - } + struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; + e = ((likely(__pyx_ptype_5pysam_6ctabix_Parser)) ? ((__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) ? __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord)); if (e) return e; if (p->vcffile) { e = (*v)(p->vcffile, a); if (e) return e; } return 0; } -static int __pyx_tp_clear_4cvcf_asVCFRecord(PyObject *o) { - struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o; +static int __pyx_tp_clear_5pysam_4cvcf_asVCFRecord(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; PyObject* tmp; - if (__pyx_ptype_6ctabix_Parser->tp_clear) { - __pyx_ptype_6ctabix_Parser->tp_clear(o); - } + if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) { if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_asVCFRecord); tmp = ((PyObject*)p->vcffile); p->vcffile = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } -static PyMethodDef __pyx_methods_4cvcf_asVCFRecord[] = { +static PyMethodDef __pyx_methods_5pysam_4cvcf_asVCFRecord[] = { {0, 0, 0, 0} }; @@ -23287,12 +23590,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asVCFRecord = { #endif }; -static PyTypeObject __pyx_type_4cvcf_asVCFRecord = { +static PyTypeObject __pyx_type_5pysam_4cvcf_asVCFRecord = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("cvcf.asVCFRecord"), /*tp_name*/ - sizeof(struct __pyx_obj_4cvcf_asVCFRecord), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.cvcf.asVCFRecord"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_4cvcf_asVCFRecord), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_4cvcf_asVCFRecord, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -23306,20 +23609,20 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = { &__pyx_tp_as_sequence_asVCFRecord, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/ 0, /*tp_hash*/ - __pyx_pw_4cvcf_11asVCFRecord_3__call__, /*tp_call*/ + __pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asVCFRecord, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/ - __pyx_tp_traverse_4cvcf_asVCFRecord, /*tp_traverse*/ - __pyx_tp_clear_4cvcf_asVCFRecord, /*tp_clear*/ + __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord, /*tp_traverse*/ + __pyx_tp_clear_5pysam_4cvcf_asVCFRecord, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_4cvcf_asVCFRecord, /*tp_methods*/ + __pyx_methods_5pysam_4cvcf_asVCFRecord, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -23327,9 +23630,9 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_4cvcf_11asVCFRecord_1__init__, /*tp_init*/ + __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_4cvcf_asVCFRecord, /*tp_new*/ + __pyx_tp_new_5pysam_4cvcf_asVCFRecord, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -23343,32 +23646,34 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = { #endif }; -static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p; +static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o); + p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o); p->__pyx_v_alt = 0; return o; } -static void __pyx_tp_dealloc_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { - struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o; - Py_XDECREF(p->__pyx_v_alt); +static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; + PyObject_GC_UnTrack(o); + Py_CLEAR(p->__pyx_v_alt); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_4cvcf___pyx_scope_struct__parse_data(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o; + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; if (p->__pyx_v_alt) { e = (*v)(p->__pyx_v_alt, a); if (e) return e; } return 0; } -static int __pyx_tp_clear_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { - struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o; +static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; PyObject* tmp; tmp = ((PyObject*)p->__pyx_v_alt); p->__pyx_v_alt = Py_None; Py_INCREF(Py_None); @@ -23376,7 +23681,7 @@ static int __pyx_tp_clear_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { return 0; } -static PyMethodDef __pyx_methods_4cvcf___pyx_scope_struct__parse_data[] = { +static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct__parse_data[] = { {0, 0, 0, 0} }; @@ -23478,12 +23783,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__parse_data = { #endif }; -static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = { +static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("cvcf.__pyx_scope_struct__parse_data"), /*tp_name*/ - sizeof(struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct__parse_data"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_4cvcf___pyx_scope_struct__parse_data, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -23504,13 +23809,13 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = { &__pyx_tp_as_buffer___pyx_scope_struct__parse_data, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ - __pyx_tp_traverse_4cvcf___pyx_scope_struct__parse_data, /*tp_traverse*/ - __pyx_tp_clear_4cvcf___pyx_scope_struct__parse_data, /*tp_clear*/ + __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_traverse*/ + __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_4cvcf___pyx_scope_struct__parse_data, /*tp_methods*/ + __pyx_methods_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -23520,7 +23825,7 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_4cvcf___pyx_scope_struct__parse_data, /*tp_new*/ + __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -23534,28 +23839,30 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = { #endif }; -static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p; +static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o); + p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o); p->__pyx_outer_scope = 0; p->__pyx_v_allele = 0; p->__pyx_t_0 = 0; return o; } -static void __pyx_tp_dealloc_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) { - struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o; - Py_XDECREF(((PyObject *)p->__pyx_outer_scope)); - Py_XDECREF(p->__pyx_v_allele); - Py_XDECREF(p->__pyx_t_0); +static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o; + PyObject_GC_UnTrack(o); + Py_CLEAR(p->__pyx_outer_scope); + Py_CLEAR(p->__pyx_v_allele); + Py_CLEAR(p->__pyx_t_0); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o; + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o; if (p->__pyx_outer_scope) { e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e; } @@ -23568,11 +23875,11 @@ static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o, vis return 0; } -static int __pyx_tp_clear_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) { - struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o; +static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o; PyObject* tmp; tmp = ((PyObject*)p->__pyx_outer_scope); - p->__pyx_outer_scope = ((struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)Py_None); Py_INCREF(Py_None); + p->__pyx_outer_scope = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->__pyx_v_allele); p->__pyx_v_allele = Py_None; Py_INCREF(Py_None); @@ -23583,7 +23890,7 @@ static int __pyx_tp_clear_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) { return 0; } -static PyMethodDef __pyx_methods_4cvcf___pyx_scope_struct_1_genexpr[] = { +static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct_1_genexpr[] = { {0, 0, 0, 0} }; @@ -23685,12 +23992,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = { #endif }; -static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = { +static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("cvcf.__pyx_scope_struct_1_genexpr"), /*tp_name*/ - sizeof(struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct_1_genexpr"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_4cvcf___pyx_scope_struct_1_genexpr, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -23711,13 +24018,13 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = { &__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ - __pyx_tp_traverse_4cvcf___pyx_scope_struct_1_genexpr, /*tp_traverse*/ - __pyx_tp_clear_4cvcf___pyx_scope_struct_1_genexpr, /*tp_clear*/ + __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_traverse*/ + __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_4cvcf___pyx_scope_struct_1_genexpr, /*tp_methods*/ + __pyx_methods_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -23727,7 +24034,7 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_4cvcf___pyx_scope_struct_1_genexpr, /*tp_new*/ + __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -23741,11 +24048,11 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = { #endif }; -static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, PyObject *a, PyObject *k) { - struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p; +static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; - p = ((struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o); + p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o); p->__pyx_v_d = 0; p->__pyx_v_line = 0; p->__pyx_v_self = 0; @@ -23754,19 +24061,21 @@ static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, return o; } -static void __pyx_tp_dealloc_4cvcf___pyx_scope_struct_2__parse(PyObject *o) { - struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o; - Py_XDECREF(p->__pyx_v_d); - Py_XDECREF(p->__pyx_v_line); - Py_XDECREF(p->__pyx_v_self); - Py_XDECREF(p->__pyx_v_stream); - Py_XDECREF(p->__pyx_t_1); +static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o; + PyObject_GC_UnTrack(o); + Py_CLEAR(p->__pyx_v_d); + Py_CLEAR(p->__pyx_v_line); + Py_CLEAR(p->__pyx_v_self); + Py_CLEAR(p->__pyx_v_stream); + Py_CLEAR(p->__pyx_t_1); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } -static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_2__parse(PyObject *o, visitproc v, void *a) { +static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o, visitproc v, void *a) { int e; - struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o; + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o; if (p->__pyx_v_d) { e = (*v)(p->__pyx_v_d, a); if (e) return e; } @@ -23785,8 +24094,8 @@ static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_2__parse(PyObject *o, visi return 0; } -static int __pyx_tp_clear_4cvcf___pyx_scope_struct_2__parse(PyObject *o) { - struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o; +static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) { + struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o; PyObject* tmp; tmp = ((PyObject*)p->__pyx_v_d); p->__pyx_v_d = Py_None; Py_INCREF(Py_None); @@ -23806,7 +24115,7 @@ static int __pyx_tp_clear_4cvcf___pyx_scope_struct_2__parse(PyObject *o) { return 0; } -static PyMethodDef __pyx_methods_4cvcf___pyx_scope_struct_2__parse[] = { +static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct_2__parse[] = { {0, 0, 0, 0} }; @@ -23908,12 +24217,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_2__parse = { #endif }; -static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_2__parse = { +static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse = { PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("cvcf.__pyx_scope_struct_2__parse"), /*tp_name*/ - sizeof(struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse), /*tp_basicsize*/ + __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct_2__parse"), /*tp_name*/ + sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse), /*tp_basicsize*/ 0, /*tp_itemsize*/ - __pyx_tp_dealloc_4cvcf___pyx_scope_struct_2__parse, /*tp_dealloc*/ + __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ @@ -23934,13 +24243,13 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_2__parse = { &__pyx_tp_as_buffer___pyx_scope_struct_2__parse, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ - __pyx_tp_traverse_4cvcf___pyx_scope_struct_2__parse, /*tp_traverse*/ - __pyx_tp_clear_4cvcf___pyx_scope_struct_2__parse, /*tp_clear*/ + __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_traverse*/ + __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ - __pyx_methods_4cvcf___pyx_scope_struct_2__parse, /*tp_methods*/ + __pyx_methods_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ @@ -23950,7 +24259,7 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_2__parse = { 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ - __pyx_tp_new_4cvcf___pyx_scope_struct_2__parse, /*tp_new*/ + __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ @@ -24002,8 +24311,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_128, __pyx_k_128, sizeof(__pyx_k_128), 0, 0, 1, 0}, {&__pyx_kp_s_130, __pyx_k_130, sizeof(__pyx_k_130), 0, 0, 1, 0}, {&__pyx_kp_s_134, __pyx_k_134, sizeof(__pyx_k_134), 0, 0, 1, 0}, - {&__pyx_kp_s_137, __pyx_k_137, sizeof(__pyx_k_137), 0, 0, 1, 0}, - {&__pyx_kp_s_139, __pyx_k_139, sizeof(__pyx_k_139), 0, 0, 1, 0}, + {&__pyx_n_s_135, __pyx_k_135, sizeof(__pyx_k_135), 0, 0, 1, 1}, + {&__pyx_kp_s_138, __pyx_k_138, sizeof(__pyx_k_138), 0, 0, 1, 0}, {&__pyx_kp_s_14, __pyx_k_14, sizeof(__pyx_k_14), 0, 0, 1, 0}, {&__pyx_kp_s_140, __pyx_k_140, sizeof(__pyx_k_140), 0, 0, 1, 0}, {&__pyx_kp_s_141, __pyx_k_141, sizeof(__pyx_k_141), 0, 0, 1, 0}, @@ -24038,6 +24347,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_170, __pyx_k_170, sizeof(__pyx_k_170), 0, 0, 1, 0}, {&__pyx_kp_s_171, __pyx_k_171, sizeof(__pyx_k_171), 0, 0, 1, 0}, {&__pyx_kp_s_172, __pyx_k_172, sizeof(__pyx_k_172), 0, 0, 1, 0}, + {&__pyx_kp_s_173, __pyx_k_173, sizeof(__pyx_k_173), 0, 0, 1, 0}, {&__pyx_n_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 1}, {&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0}, {&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0}, @@ -24219,7 +24529,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s__convertGT, __pyx_k__convertGT, sizeof(__pyx_k__convertGT), 0, 0, 1, 1}, {&__pyx_n_s__convertGTback, __pyx_k__convertGTback, sizeof(__pyx_k__convertGTback), 0, 0, 1, 1}, {&__pyx_n_s__copy, __pyx_k__copy, sizeof(__pyx_k__copy), 0, 0, 1, 1}, - {&__pyx_n_s__cvcf, __pyx_k__cvcf, sizeof(__pyx_k__cvcf), 0, 0, 1, 1}, {&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1}, {&__pyx_n_s__data, __pyx_k__data, sizeof(__pyx_k__data), 0, 0, 1, 1}, {&__pyx_n_s__datagenerator, __pyx_k__datagenerator, sizeof(__pyx_k__datagenerator), 0, 0, 1, 1}, @@ -24401,7 +24710,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "cvcf.pyx":70 + /* "pysam/cvcf.pyx":70 * def parse_regions( string ): * result = [] * for r in string.split(','): # <<<<<<<<<<<<<< @@ -24415,7 +24724,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_3)); - /* "cvcf.pyx":71 + /* "pysam/cvcf.pyx":71 * result = [] * for r in string.split(','): * elts = r.split(':') # <<<<<<<<<<<<<< @@ -24429,7 +24738,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_5)); - /* "cvcf.pyx":76 + /* "pysam/cvcf.pyx":76 * elif len(elts)==2: * if len(elts[1])>0: * ielts = elts[1].split('-') # <<<<<<<<<<<<<< @@ -24443,7 +24752,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_7)); - /* "cvcf.pyx":157 + /* "pysam/cvcf.pyx":157 * alt = self.fields[4] * if alt == ".": alt = [] * else: alt = alt.upper().split(',') # <<<<<<<<<<<<<< @@ -24457,7 +24766,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10)); - /* "cvcf.pyx":173 + /* "pysam/cvcf.pyx":173 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list * if f == b"." or f == b"PASS" or f == b"0": return [] * else: return f.split(';') # <<<<<<<<<<<<<< @@ -24471,7 +24780,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12)); - /* "cvcf.pyx":181 + /* "pysam/cvcf.pyx":181 * info = {} * if col != b".": * for blurp in col.split(';'): # <<<<<<<<<<<<<< @@ -24485,7 +24794,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13)); - /* "cvcf.pyx":182 + /* "pysam/cvcf.pyx":182 * if col != b".": * for blurp in col.split(';'): * elts = blurp.split('=') # <<<<<<<<<<<<<< @@ -24499,7 +24808,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15)); - /* "cvcf.pyx":191 + /* "pysam/cvcf.pyx":191 * property format: * def __get__(self): * return self.fields[8].split(':') # <<<<<<<<<<<<<< @@ -24513,7 +24822,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_16)); - /* "cvcf.pyx":200 + /* "pysam/cvcf.pyx":200 * * # parse sample columns * values = self.fields[self.vcf._sample2column[key]].split(':') # <<<<<<<<<<<<<< @@ -24527,7 +24836,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_17)); - /* "cvcf.pyx":316 + /* "pysam/cvcf.pyx":316 * def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): * # make error identifiers accessible by name * for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id # <<<<<<<<<<<<<< @@ -24541,7 +24850,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_22)); - /* "cvcf.pyx":337 + /* "pysam/cvcf.pyx":337 * def error(self,line,error,opt=None): * if error in self._ignored_errors: return * errorlabel, errorstring = self._errors[error].split(':') # <<<<<<<<<<<<<< @@ -24555,7 +24864,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23)); - /* "cvcf.pyx":346 + /* "pysam/cvcf.pyx":346 * def parse_format(self,line,format,filter=False): * if self._version == 40: * if not format.startswith('<'): # <<<<<<<<<<<<<< @@ -24569,7 +24878,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26)); - /* "cvcf.pyx":349 + /* "pysam/cvcf.pyx":349 * self.error(line,self.V40_MISSING_ANGLE_BRACKETS) * format = "<"+format * if not format.endswith('>'): # <<<<<<<<<<<<<< @@ -24583,7 +24892,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_28)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_29)); - /* "cvcf.pyx":356 + /* "pysam/cvcf.pyx":356 * idx = 0 * while len(format.strip())>0: * elts = format.strip().split(',') # <<<<<<<<<<<<<< @@ -24597,7 +24906,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_30)); - /* "cvcf.pyx":358 + /* "pysam/cvcf.pyx":358 * elts = format.strip().split(',') * first, rest = elts[0], ','.join(elts[1:]) * if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): # <<<<<<<<<<<<<< @@ -24629,7 +24938,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35)); - /* "cvcf.pyx":362 + /* "pysam/cvcf.pyx":362 * if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) * first = ["ID=","Number=","Type=","Description="][idx] + first * if first.startswith('ID='): data['id'] = first.split('=')[1] # <<<<<<<<<<<<<< @@ -24649,7 +24958,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_43)); - /* "cvcf.pyx":363 + /* "pysam/cvcf.pyx":363 * first = ["ID=","Number=","Type=","Description="][idx] + first * if first.startswith('ID='): data['id'] = first.split('=')[1] * elif first.startswith('Number='): data['number'] = first.split('=')[1] # <<<<<<<<<<<<<< @@ -24669,7 +24978,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_45)); - /* "cvcf.pyx":364 + /* "pysam/cvcf.pyx":364 * if first.startswith('ID='): data['id'] = first.split('=')[1] * elif first.startswith('Number='): data['number'] = first.split('=')[1] * elif first.startswith('Type='): data['type'] = first.split('=')[1] # <<<<<<<<<<<<<< @@ -24689,7 +24998,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47)); - /* "cvcf.pyx":365 + /* "pysam/cvcf.pyx":365 * elif first.startswith('Number='): data['number'] = first.split('=')[1] * elif first.startswith('Type='): data['type'] = first.split('=')[1] * elif first.startswith('Description='): # <<<<<<<<<<<<<< @@ -24703,7 +25012,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_41)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48)); - /* "cvcf.pyx":366 + /* "pysam/cvcf.pyx":366 * elif first.startswith('Type='): data['type'] = first.split('=')[1] * elif first.startswith('Description='): * elts = format.split('"') # <<<<<<<<<<<<<< @@ -24717,7 +25026,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49)); - /* "cvcf.pyx":369 + /* "pysam/cvcf.pyx":369 * if len(elts)<3: * self.error(line,self.FORMAT_MISSING_QUOTES) * elts = first.split('=') + [rest] # <<<<<<<<<<<<<< @@ -24731,7 +25040,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51)); - /* "cvcf.pyx":372 + /* "pysam/cvcf.pyx":372 * data['descr'] = elts[1] * rest = '"'.join(elts[2:]) * if rest.startswith(','): rest = rest[1:] # <<<<<<<<<<<<<< @@ -24745,7 +25054,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52)); - /* "cvcf.pyx":492 + /* "pysam/cvcf.pyx":492 * # snip off trailing missing data * while len(output) > 1: * last = output[-1].replace(',','').replace('.','') # <<<<<<<<<<<<<< @@ -24771,7 +25080,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_1)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63)); - /* "cvcf.pyx":518 + /* "pysam/cvcf.pyx":518 * * def parse_header( self, line ): * assert line.startswith('##') # <<<<<<<<<<<<<< @@ -24785,7 +25094,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77)); - /* "cvcf.pyx":519 + /* "pysam/cvcf.pyx":519 * def parse_header( self, line ): * assert line.startswith('##') * elts = line[2:].split('=') # <<<<<<<<<<<<<< @@ -24799,7 +25108,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78)); - /* "cvcf.pyx":554 + /* "pysam/cvcf.pyx":554 * * def parse_heading( self, line ): * assert line.startswith('#') # <<<<<<<<<<<<<< @@ -24813,7 +25122,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86)); - /* "cvcf.pyx":555 + /* "pysam/cvcf.pyx":555 * def parse_heading( self, line ): * assert line.startswith('#') * assert not line.startswith('##') # <<<<<<<<<<<<<< @@ -24827,7 +25136,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87)); - /* "cvcf.pyx":556 + /* "pysam/cvcf.pyx":556 * assert line.startswith('#') * assert not line.startswith('##') * headings = line[1:].split('\t') # <<<<<<<<<<<<<< @@ -24841,7 +25150,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_88)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89)); - /* "cvcf.pyx":608 + /* "pysam/cvcf.pyx":608 * if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) * return [] * values = value.split(',') # <<<<<<<<<<<<<< @@ -24855,7 +25164,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97)); - /* "cvcf.pyx":610 + /* "pysam/cvcf.pyx":610 * values = value.split(',') * # deal with trailing data in some early VCF files * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: # <<<<<<<<<<<<<< @@ -24869,7 +25178,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98)); - /* "cvcf.pyx":612 + /* "pysam/cvcf.pyx":612 * if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: * self.error(line,self.ERROR_TRAILING_DATA,values[-1]) * values[-1] = values[-1].split(';')[0] # <<<<<<<<<<<<<< @@ -24883,7 +25192,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99)); - /* "cvcf.pyx":648 + /* "pysam/cvcf.pyx":648 * * def parse_data( self, line, lineparse=False ): * cols = line.split('\t') # <<<<<<<<<<<<<< @@ -24897,7 +25206,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_88)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103)); - /* "cvcf.pyx":694 + /* "pysam/cvcf.pyx":694 * # convert v3.3 to v4.0 alleles below * if cols[4] == ".": alt = [] * else: alt = cols[4].upper().split(',') # <<<<<<<<<<<<<< @@ -24911,7 +25220,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_107)); - /* "cvcf.pyx":703 + /* "pysam/cvcf.pyx":703 * # postpone checking that filters exist. Encode missing filter or no filtering as empty list * if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] * else: filter = cols[6].split(';') # <<<<<<<<<<<<<< @@ -24925,7 +25234,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_108)); - /* "cvcf.pyx":708 + /* "pysam/cvcf.pyx":708 * info = {} * if cols[7] != ".": * for blurp in cols[7].split(';'): # <<<<<<<<<<<<<< @@ -24939,7 +25248,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_109)); - /* "cvcf.pyx":709 + /* "pysam/cvcf.pyx":709 * if cols[7] != ".": * for blurp in cols[7].split(';'): * elts = blurp.split('=') # <<<<<<<<<<<<<< @@ -24953,7 +25262,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_110)); - /* "cvcf.pyx":720 + /* "pysam/cvcf.pyx":720 * # Gracefully deal with absent FORMAT column * if cols[8] == "": format = [] * else: format = cols[8].split(':') # <<<<<<<<<<<<<< @@ -24967,7 +25276,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_111)); - /* "cvcf.pyx":738 + /* "pysam/cvcf.pyx":738 * for a in alt: * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference # <<<<<<<<<<<<<< @@ -24981,7 +25290,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_n_s__I)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_112)); - /* "cvcf.pyx":739 + /* "pysam/cvcf.pyx":739 * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference * elif a.startswith('D'): # allow D and D # <<<<<<<<<<<<<< @@ -24995,7 +25304,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_n_s__D)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_113)); - /* "cvcf.pyx":820 + /* "pysam/cvcf.pyx":820 * for sample in cols[9:]: * dict = {} * values = sample.split(':') # <<<<<<<<<<<<<< @@ -25009,7 +25318,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117)); - /* "cvcf.pyx":890 + /* "pysam/cvcf.pyx":890 * for line in stream: * self._lineno += 1 * if line.startswith('##'): # <<<<<<<<<<<<<< @@ -25023,7 +25332,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_119)); - /* "cvcf.pyx":892 + /* "pysam/cvcf.pyx":892 * if line.startswith('##'): * self.parse_header( line.strip() ) * elif line.startswith('#'): # <<<<<<<<<<<<<< @@ -25037,7 +25346,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_120)); - /* "cvcf.pyx":901 + /* "pysam/cvcf.pyx":901 * def _parse(self, line, stream): * # deal with files with header only * if line.startswith("##"): return # <<<<<<<<<<<<<< @@ -25051,7 +25360,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122)); - /* "cvcf.pyx":958 + /* "pysam/cvcf.pyx":958 * * def setversion(self, version): * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") # <<<<<<<<<<<<<< @@ -25065,7 +25374,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_123)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124)); - /* "cvcf.pyx":1036 + /* "pysam/cvcf.pyx":1036 * ''' * * raise NotImplementedError( "needs to be checked" ) # <<<<<<<<<<<<<< @@ -25079,7 +25388,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_126)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_127)); - /* "cvcf.pyx":54 + /* "pysam/cvcf.pyx":54 * import pysam * * gtsRegEx = re.compile("[|/\\\\]") # <<<<<<<<<<<<<< @@ -25093,7 +25402,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_128)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_129)); - /* "cvcf.pyx":55 + /* "pysam/cvcf.pyx":55 * * gtsRegEx = re.compile("[|/\\\\]") * alleleRegEx = re.compile('^[ACGTN]+$') # <<<<<<<<<<<<<< @@ -25107,7 +25416,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_130)); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_131)); - /* "cvcf.pyx":58 + /* "pysam/cvcf.pyx":58 * * # Utility function. Uses 0-based coordinates * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<< @@ -25134,1216 +25443,1216 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_132)); __pyx_k_codeobj_133 = (PyObject*)__Pyx_PyCode_New(4, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_132, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__get_sequence, 58, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":68 + /* "pysam/cvcf.pyx":68 * * # Utility function. Parses a region string * def parse_regions( string ): # <<<<<<<<<<<<<< * result = [] * for r in string.split(','): */ - __pyx_k_tuple_135 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_135)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_135); + __pyx_k_tuple_136 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_136)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_136); __Pyx_INCREF(((PyObject *)__pyx_n_s__string)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 0, ((PyObject *)__pyx_n_s__string)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 0, ((PyObject *)__pyx_n_s__string)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__string)); __Pyx_INCREF(((PyObject *)__pyx_n_s__result)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 1, ((PyObject *)__pyx_n_s__result)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 1, ((PyObject *)__pyx_n_s__result)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__result)); __Pyx_INCREF(((PyObject *)__pyx_n_s__r)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 2, ((PyObject *)__pyx_n_s__r)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 2, ((PyObject *)__pyx_n_s__r)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r)); __Pyx_INCREF(((PyObject *)__pyx_n_s__elts)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 3, ((PyObject *)__pyx_n_s__elts)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 3, ((PyObject *)__pyx_n_s__elts)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts)); __Pyx_INCREF(((PyObject *)__pyx_n_s__chrom)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 4, ((PyObject *)__pyx_n_s__chrom)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 4, ((PyObject *)__pyx_n_s__chrom)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__chrom)); __Pyx_INCREF(((PyObject *)__pyx_n_s__start)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 5, ((PyObject *)__pyx_n_s__start)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 5, ((PyObject *)__pyx_n_s__start)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__start)); __Pyx_INCREF(((PyObject *)__pyx_n_s__end)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 6, ((PyObject *)__pyx_n_s__end)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 6, ((PyObject *)__pyx_n_s__end)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__end)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ielts)); - PyTuple_SET_ITEM(__pyx_k_tuple_135, 7, ((PyObject *)__pyx_n_s__ielts)); + PyTuple_SET_ITEM(__pyx_k_tuple_136, 7, ((PyObject *)__pyx_n_s__ielts)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ielts)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_135)); - __pyx_k_codeobj_136 = (PyObject*)__Pyx_PyCode_New(1, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_135, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_regions, 68, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_136)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_136)); + __pyx_k_codeobj_137 = (PyObject*)__Pyx_PyCode_New(1, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_136, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_regions, 68, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_137)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":86 + /* "pysam/cvcf.pyx":86 * * * FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') # <<<<<<<<<<<<<< * * ########################################################################################################### */ - __pyx_k_tuple_138 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_138)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_138); + __pyx_k_tuple_139 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_139)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_139); __Pyx_INCREF(((PyObject *)__pyx_n_s__FORMAT)); - PyTuple_SET_ITEM(__pyx_k_tuple_138, 0, ((PyObject *)__pyx_n_s__FORMAT)); + PyTuple_SET_ITEM(__pyx_k_tuple_139, 0, ((PyObject *)__pyx_n_s__FORMAT)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__FORMAT)); - __Pyx_INCREF(((PyObject *)__pyx_kp_s_137)); - PyTuple_SET_ITEM(__pyx_k_tuple_138, 1, ((PyObject *)__pyx_kp_s_137)); - __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_137)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_138)); + __Pyx_INCREF(((PyObject *)__pyx_kp_s_138)); + PyTuple_SET_ITEM(__pyx_k_tuple_139, 1, ((PyObject *)__pyx_kp_s_138)); + __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_138)); + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_139)); - /* "cvcf.pyx":314 + /* "pysam/cvcf.pyx":314 * _lines = None * * def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # <<<<<<<<<<<<<< * # make error identifiers accessible by name * for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id */ - __pyx_k_tuple_173 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_173)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_173); + __pyx_k_tuple_174 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_174); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_173, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_174, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s___copy)); - PyTuple_SET_ITEM(__pyx_k_tuple_173, 1, ((PyObject *)__pyx_n_s___copy)); + PyTuple_SET_ITEM(__pyx_k_tuple_174, 1, ((PyObject *)__pyx_n_s___copy)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s___copy)); __Pyx_INCREF(((PyObject *)__pyx_n_s__reference)); - PyTuple_SET_ITEM(__pyx_k_tuple_173, 2, ((PyObject *)__pyx_n_s__reference)); + PyTuple_SET_ITEM(__pyx_k_tuple_174, 2, ((PyObject *)__pyx_n_s__reference)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__reference)); __Pyx_INCREF(((PyObject *)__pyx_n_s__regions)); - PyTuple_SET_ITEM(__pyx_k_tuple_173, 3, ((PyObject *)__pyx_n_s__regions)); + PyTuple_SET_ITEM(__pyx_k_tuple_174, 3, ((PyObject *)__pyx_n_s__regions)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__regions)); __Pyx_INCREF(((PyObject *)__pyx_n_s__lines)); - PyTuple_SET_ITEM(__pyx_k_tuple_173, 4, ((PyObject *)__pyx_n_s__lines)); + PyTuple_SET_ITEM(__pyx_k_tuple_174, 4, ((PyObject *)__pyx_n_s__lines)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__lines)); __Pyx_INCREF(((PyObject *)__pyx_n_s__leftalign)); - PyTuple_SET_ITEM(__pyx_k_tuple_173, 5, ((PyObject *)__pyx_n_s__leftalign)); + PyTuple_SET_ITEM(__pyx_k_tuple_174, 5, ((PyObject *)__pyx_n_s__leftalign)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__leftalign)); __Pyx_INCREF(((PyObject *)__pyx_n_s__id)); - PyTuple_SET_ITEM(__pyx_k_tuple_173, 6, ((PyObject *)__pyx_n_s__id)); + PyTuple_SET_ITEM(__pyx_k_tuple_174, 6, ((PyObject *)__pyx_n_s__id)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__id)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_173)); - __pyx_k_codeobj_174 = (PyObject*)__Pyx_PyCode_New(6, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_173, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s____init__, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_174)); + __pyx_k_codeobj_175 = (PyObject*)__Pyx_PyCode_New(6, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_174, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s____init__, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":335 + /* "pysam/cvcf.pyx":335 * self._lines = lines * * def error(self,line,error,opt=None): # <<<<<<<<<<<<<< * if error in self._ignored_errors: return * errorlabel, errorstring = self._errors[error].split(':') */ - __pyx_k_tuple_175 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_175); + __pyx_k_tuple_176 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_176)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_176); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_175, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_176, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_175, 1, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_176, 1, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__error)); - PyTuple_SET_ITEM(__pyx_k_tuple_175, 2, ((PyObject *)__pyx_n_s__error)); + PyTuple_SET_ITEM(__pyx_k_tuple_176, 2, ((PyObject *)__pyx_n_s__error)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__error)); __Pyx_INCREF(((PyObject *)__pyx_n_s__opt)); - PyTuple_SET_ITEM(__pyx_k_tuple_175, 3, ((PyObject *)__pyx_n_s__opt)); + PyTuple_SET_ITEM(__pyx_k_tuple_176, 3, ((PyObject *)__pyx_n_s__opt)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__opt)); __Pyx_INCREF(((PyObject *)__pyx_n_s__errorlabel)); - PyTuple_SET_ITEM(__pyx_k_tuple_175, 4, ((PyObject *)__pyx_n_s__errorlabel)); + PyTuple_SET_ITEM(__pyx_k_tuple_176, 4, ((PyObject *)__pyx_n_s__errorlabel)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorlabel)); __Pyx_INCREF(((PyObject *)__pyx_n_s__errorstring)); - PyTuple_SET_ITEM(__pyx_k_tuple_175, 5, ((PyObject *)__pyx_n_s__errorstring)); + PyTuple_SET_ITEM(__pyx_k_tuple_176, 5, ((PyObject *)__pyx_n_s__errorstring)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorstring)); __Pyx_INCREF(((PyObject *)__pyx_n_s__errwarn)); - PyTuple_SET_ITEM(__pyx_k_tuple_175, 6, ((PyObject *)__pyx_n_s__errwarn)); + PyTuple_SET_ITEM(__pyx_k_tuple_176, 6, ((PyObject *)__pyx_n_s__errwarn)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errwarn)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_175)); - __pyx_k_codeobj_176 = (PyObject*)__Pyx_PyCode_New(4, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_175, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__error, 335, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_176)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_k_tuple_177 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_177)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_177); + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_176)); + __pyx_k_codeobj_177 = (PyObject*)__Pyx_PyCode_New(4, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_176, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__error, 335, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_177)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_k_tuple_178 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_178)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_178); __Pyx_INCREF(((PyObject *)Py_None)); - PyTuple_SET_ITEM(__pyx_k_tuple_177, 0, ((PyObject *)Py_None)); + PyTuple_SET_ITEM(__pyx_k_tuple_178, 0, ((PyObject *)Py_None)); __Pyx_GIVEREF(((PyObject *)Py_None)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_177)); + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_178)); - /* "cvcf.pyx":344 + /* "pysam/cvcf.pyx":344 * raise ValueError(errorstring) * * def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<< * if self._version == 40: * if not format.startswith('<'): */ - __pyx_k_tuple_178 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_178)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_178); + __pyx_k_tuple_179 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_179)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_179); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 1, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 1, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__format)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 2, ((PyObject *)__pyx_n_s__format)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 2, ((PyObject *)__pyx_n_s__format)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format)); __Pyx_INCREF(((PyObject *)__pyx_n_s__filter)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 3, ((PyObject *)__pyx_n_s__filter)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 3, ((PyObject *)__pyx_n_s__filter)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter)); __Pyx_INCREF(((PyObject *)__pyx_n_s__data)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 4, ((PyObject *)__pyx_n_s__data)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 4, ((PyObject *)__pyx_n_s__data)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data)); __Pyx_INCREF(((PyObject *)__pyx_n_s__idx)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 5, ((PyObject *)__pyx_n_s__idx)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 5, ((PyObject *)__pyx_n_s__idx)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx)); __Pyx_INCREF(((PyObject *)__pyx_n_s__elts)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 6, ((PyObject *)__pyx_n_s__elts)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 6, ((PyObject *)__pyx_n_s__elts)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts)); __Pyx_INCREF(((PyObject *)__pyx_n_s__first)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 7, ((PyObject *)__pyx_n_s__first)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 7, ((PyObject *)__pyx_n_s__first)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__first)); __Pyx_INCREF(((PyObject *)__pyx_n_s__rest)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 8, ((PyObject *)__pyx_n_s__rest)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 8, ((PyObject *)__pyx_n_s__rest)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rest)); __Pyx_INCREF(((PyObject *)__pyx_n_s__n)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 9, ((PyObject *)__pyx_n_s__n)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 9, ((PyObject *)__pyx_n_s__n)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n)); __Pyx_INCREF(((PyObject *)__pyx_n_s__t)); - PyTuple_SET_ITEM(__pyx_k_tuple_178, 10, ((PyObject *)__pyx_n_s__t)); + PyTuple_SET_ITEM(__pyx_k_tuple_179, 10, ((PyObject *)__pyx_n_s__t)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__t)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_178)); - __pyx_k_codeobj_179 = (PyObject*)__Pyx_PyCode_New(4, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_178, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_format, 344, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_179)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_179)); + __pyx_k_codeobj_180 = (PyObject*)__Pyx_PyCode_New(4, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_179, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_format, 344, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_180)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":416 + /* "pysam/cvcf.pyx":416 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) * * def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<< * values = [('ID',fmt.id)] * if fmt.number != None and not filter: */ - __pyx_k_tuple_180 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_180)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_180); + __pyx_k_tuple_181 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_181); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__fmt)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 1, ((PyObject *)__pyx_n_s__fmt)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 1, ((PyObject *)__pyx_n_s__fmt)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fmt)); __Pyx_INCREF(((PyObject *)__pyx_n_s__filter)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 2, ((PyObject *)__pyx_n_s__filter)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 2, ((PyObject *)__pyx_n_s__filter)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter)); __Pyx_INCREF(((PyObject *)__pyx_n_s__values)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 3, ((PyObject *)__pyx_n_s__values)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 3, ((PyObject *)__pyx_n_s__values)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__values)); __Pyx_INCREF(((PyObject *)__pyx_n_s__nmb)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 4, ((PyObject *)__pyx_n_s__nmb)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 4, ((PyObject *)__pyx_n_s__nmb)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__nmb)); __Pyx_INCREF(((PyObject *)__pyx_n_s__format)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 5, ((PyObject *)__pyx_n_s__format)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 5, ((PyObject *)__pyx_n_s__format)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format)); __Pyx_INCREF(((PyObject *)__pyx_n_s__k)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 6, ((PyObject *)__pyx_n_s__k)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 6, ((PyObject *)__pyx_n_s__k)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__k)); __Pyx_INCREF(((PyObject *)__pyx_n_s__v)); - PyTuple_SET_ITEM(__pyx_k_tuple_180, 7, ((PyObject *)__pyx_n_s__v)); + PyTuple_SET_ITEM(__pyx_k_tuple_181, 7, ((PyObject *)__pyx_n_s__v)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_180)); - __pyx_k_codeobj_181 = (PyObject*)__Pyx_PyCode_New(3, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_180, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_format, 416, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_181)); + __pyx_k_codeobj_182 = (PyObject*)__Pyx_PyCode_New(3, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_181, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_format, 416, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":436 + /* "pysam/cvcf.pyx":436 * return format * * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<< * fmt = formatdict[format] * if fmt.numbertype == self.NT_UNKNOWN: return -1 */ - __pyx_k_tuple_182 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_182); + __pyx_k_tuple_183 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_183); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_182, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_183, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__format)); - PyTuple_SET_ITEM(__pyx_k_tuple_182, 1, ((PyObject *)__pyx_n_s__format)); + PyTuple_SET_ITEM(__pyx_k_tuple_183, 1, ((PyObject *)__pyx_n_s__format)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format)); __Pyx_INCREF(((PyObject *)__pyx_n_s__formatdict)); - PyTuple_SET_ITEM(__pyx_k_tuple_182, 2, ((PyObject *)__pyx_n_s__formatdict)); + PyTuple_SET_ITEM(__pyx_k_tuple_183, 2, ((PyObject *)__pyx_n_s__formatdict)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__formatdict)); __Pyx_INCREF(((PyObject *)__pyx_n_s__alt)); - PyTuple_SET_ITEM(__pyx_k_tuple_182, 3, ((PyObject *)__pyx_n_s__alt)); + PyTuple_SET_ITEM(__pyx_k_tuple_183, 3, ((PyObject *)__pyx_n_s__alt)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt)); __Pyx_INCREF(((PyObject *)__pyx_n_s__fmt)); - PyTuple_SET_ITEM(__pyx_k_tuple_182, 4, ((PyObject *)__pyx_n_s__fmt)); + PyTuple_SET_ITEM(__pyx_k_tuple_183, 4, ((PyObject *)__pyx_n_s__fmt)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fmt)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_182)); - __pyx_k_codeobj_183 = (PyObject*)__Pyx_PyCode_New(4, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_182, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__get_expected, 436, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_183)); + __pyx_k_codeobj_184 = (PyObject*)__Pyx_PyCode_New(4, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_183, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__get_expected, 436, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":447 + /* "pysam/cvcf.pyx":447 * * * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<< * if key in formatdict: return * self.error(line,self.ERROR_UNKNOWN_KEY,key) */ - __pyx_k_tuple_184 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_184); + __pyx_k_tuple_185 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_185)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_185); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_184, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_185, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__formatdict)); - PyTuple_SET_ITEM(__pyx_k_tuple_184, 1, ((PyObject *)__pyx_n_s__formatdict)); + PyTuple_SET_ITEM(__pyx_k_tuple_185, 1, ((PyObject *)__pyx_n_s__formatdict)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__formatdict)); __Pyx_INCREF(((PyObject *)__pyx_n_s__key)); - PyTuple_SET_ITEM(__pyx_k_tuple_184, 2, ((PyObject *)__pyx_n_s__key)); + PyTuple_SET_ITEM(__pyx_k_tuple_185, 2, ((PyObject *)__pyx_n_s__key)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key)); __Pyx_INCREF(((PyObject *)__pyx_n_s__data)); - PyTuple_SET_ITEM(__pyx_k_tuple_184, 3, ((PyObject *)__pyx_n_s__data)); + PyTuple_SET_ITEM(__pyx_k_tuple_185, 3, ((PyObject *)__pyx_n_s__data)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_184, 4, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_185, 4, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_184)); - __pyx_k_codeobj_185 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_184, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___add_definition, 447, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_185)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_185)); + __pyx_k_codeobj_186 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_185, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___add_definition, 447, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_186)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":464 + /* "pysam/cvcf.pyx":464 * * # todo: trim trailing missing values * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<< * output, sdata = [], [] * if type(data) == type([]): # for FORMAT field, make data with dummy values */ - __pyx_k_tuple_186 = PyTuple_New(13); if (unlikely(!__pyx_k_tuple_186)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_186); + __pyx_k_tuple_187 = PyTuple_New(13); if (unlikely(!__pyx_k_tuple_187)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_187); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__data)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 1, ((PyObject *)__pyx_n_s__data)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 1, ((PyObject *)__pyx_n_s__data)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data)); __Pyx_INCREF(((PyObject *)__pyx_n_s__format)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 2, ((PyObject *)__pyx_n_s__format)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 2, ((PyObject *)__pyx_n_s__format)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format)); __Pyx_INCREF(((PyObject *)__pyx_n_s__key)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 3, ((PyObject *)__pyx_n_s__key)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 3, ((PyObject *)__pyx_n_s__key)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key)); __Pyx_INCREF(((PyObject *)__pyx_n_s__value)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 4, ((PyObject *)__pyx_n_s__value)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 4, ((PyObject *)__pyx_n_s__value)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value)); __Pyx_INCREF(((PyObject *)__pyx_n_s__separator)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 5, ((PyObject *)__pyx_n_s__separator)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 5, ((PyObject *)__pyx_n_s__separator)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__separator)); __Pyx_INCREF(((PyObject *)__pyx_n_s__output)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 6, ((PyObject *)__pyx_n_s__output)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 6, ((PyObject *)__pyx_n_s__output)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__output)); __Pyx_INCREF(((PyObject *)__pyx_n_s__sdata)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 7, ((PyObject *)__pyx_n_s__sdata)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 7, ((PyObject *)__pyx_n_s__sdata)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__sdata)); __Pyx_INCREF(((PyObject *)__pyx_n_s__d)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 8, ((PyObject *)__pyx_n_s__d)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 8, ((PyObject *)__pyx_n_s__d)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__d)); __Pyx_INCREF(((PyObject *)__pyx_n_s__k)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 9, ((PyObject *)__pyx_n_s__k)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 9, ((PyObject *)__pyx_n_s__k)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__k)); __Pyx_INCREF(((PyObject *)__pyx_n_s__idx)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 10, ((PyObject *)__pyx_n_s__idx)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 10, ((PyObject *)__pyx_n_s__idx)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx)); __Pyx_INCREF(((PyObject *)__pyx_n_s__v)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 11, ((PyObject *)__pyx_n_s__v)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 11, ((PyObject *)__pyx_n_s__v)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v)); __Pyx_INCREF(((PyObject *)__pyx_n_s__last)); - PyTuple_SET_ITEM(__pyx_k_tuple_186, 12, ((PyObject *)__pyx_n_s__last)); + PyTuple_SET_ITEM(__pyx_k_tuple_187, 12, ((PyObject *)__pyx_n_s__last)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__last)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_186)); - __pyx_k_codeobj_187 = (PyObject*)__Pyx_PyCode_New(6, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_186, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_formatdata, 464, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_187)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_187)); + __pyx_k_codeobj_188 = (PyObject*)__Pyx_PyCode_New(6, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_187, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_formatdata, 464, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_188)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":498 + /* "pysam/cvcf.pyx":498 * * * def enter_default_format(self): # <<<<<<<<<<<<<< * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), */ - __pyx_k_tuple_188 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_188)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_188); + __pyx_k_tuple_189 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_189)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_189); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_188, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_189, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__f)); - PyTuple_SET_ITEM(__pyx_k_tuple_188, 1, ((PyObject *)__pyx_n_s__f)); + PyTuple_SET_ITEM(__pyx_k_tuple_189, 1, ((PyObject *)__pyx_n_s__f)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_188)); - __pyx_k_codeobj_189 = (PyObject*)__Pyx_PyCode_New(1, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_188, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s_121, 498, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_189)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_189)); + __pyx_k_codeobj_190 = (PyObject*)__Pyx_PyCode_New(1, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_189, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s_121, 498, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_190)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":517 + /* "pysam/cvcf.pyx":517 * self._format[f.id] = f * * def parse_header( self, line ): # <<<<<<<<<<<<<< * assert line.startswith('##') * elts = line[2:].split('=') */ - __pyx_k_tuple_190 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_190)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_190); + __pyx_k_tuple_191 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_191)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_191); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_190, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_191, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_190, 1, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_191, 1, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__elts)); - PyTuple_SET_ITEM(__pyx_k_tuple_190, 2, ((PyObject *)__pyx_n_s__elts)); + PyTuple_SET_ITEM(__pyx_k_tuple_191, 2, ((PyObject *)__pyx_n_s__elts)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts)); __Pyx_INCREF(((PyObject *)__pyx_n_s__key)); - PyTuple_SET_ITEM(__pyx_k_tuple_190, 3, ((PyObject *)__pyx_n_s__key)); + PyTuple_SET_ITEM(__pyx_k_tuple_191, 3, ((PyObject *)__pyx_n_s__key)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key)); __Pyx_INCREF(((PyObject *)__pyx_n_s__value)); - PyTuple_SET_ITEM(__pyx_k_tuple_190, 4, ((PyObject *)__pyx_n_s__value)); + PyTuple_SET_ITEM(__pyx_k_tuple_191, 4, ((PyObject *)__pyx_n_s__value)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value)); __Pyx_INCREF(((PyObject *)__pyx_n_s__f)); - PyTuple_SET_ITEM(__pyx_k_tuple_190, 5, ((PyObject *)__pyx_n_s__f)); + PyTuple_SET_ITEM(__pyx_k_tuple_191, 5, ((PyObject *)__pyx_n_s__f)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_190)); - __pyx_k_codeobj_191 = (PyObject*)__Pyx_PyCode_New(2, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_190, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_header, 517, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_191)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_191)); + __pyx_k_codeobj_192 = (PyObject*)__Pyx_PyCode_New(2, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_191, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_header, 517, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_192)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":546 + /* "pysam/cvcf.pyx":546 * * * def write_header( self, stream ): # <<<<<<<<<<<<<< * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) * for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) */ - __pyx_k_tuple_192 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_192)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_192); + __pyx_k_tuple_193 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_193)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_193); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_192, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_193, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_192, 1, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_193, 1, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); __Pyx_INCREF(((PyObject *)__pyx_n_s__key)); - PyTuple_SET_ITEM(__pyx_k_tuple_192, 2, ((PyObject *)__pyx_n_s__key)); + PyTuple_SET_ITEM(__pyx_k_tuple_193, 2, ((PyObject *)__pyx_n_s__key)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key)); __Pyx_INCREF(((PyObject *)__pyx_n_s__value)); - PyTuple_SET_ITEM(__pyx_k_tuple_192, 3, ((PyObject *)__pyx_n_s__value)); + PyTuple_SET_ITEM(__pyx_k_tuple_193, 3, ((PyObject *)__pyx_n_s__value)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value)); __Pyx_INCREF(((PyObject *)__pyx_n_s__var)); - PyTuple_SET_ITEM(__pyx_k_tuple_192, 4, ((PyObject *)__pyx_n_s__var)); + PyTuple_SET_ITEM(__pyx_k_tuple_193, 4, ((PyObject *)__pyx_n_s__var)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__var)); __Pyx_INCREF(((PyObject *)__pyx_n_s__label)); - PyTuple_SET_ITEM(__pyx_k_tuple_192, 5, ((PyObject *)__pyx_n_s__label)); + PyTuple_SET_ITEM(__pyx_k_tuple_193, 5, ((PyObject *)__pyx_n_s__label)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__label)); __Pyx_INCREF(((PyObject *)__pyx_n_s__f)); - PyTuple_SET_ITEM(__pyx_k_tuple_192, 6, ((PyObject *)__pyx_n_s__f)); + PyTuple_SET_ITEM(__pyx_k_tuple_193, 6, ((PyObject *)__pyx_n_s__f)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_192)); - __pyx_k_codeobj_193 = (PyObject*)__Pyx_PyCode_New(2, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_192, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_header, 546, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_193)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_193)); + __pyx_k_codeobj_194 = (PyObject*)__Pyx_PyCode_New(2, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_193, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_header, 546, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_194)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":553 + /* "pysam/cvcf.pyx":553 * * * def parse_heading( self, line ): # <<<<<<<<<<<<<< * assert line.startswith('#') * assert not line.startswith('##') */ - __pyx_k_tuple_194 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_194)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_194); + __pyx_k_tuple_195 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_195)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_195); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 1, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 1, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__headings)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 2, ((PyObject *)__pyx_n_s__headings)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 2, ((PyObject *)__pyx_n_s__headings)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__headings)); __Pyx_INCREF(((PyObject *)__pyx_n_s__i)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 3, ((PyObject *)__pyx_n_s__i)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 3, ((PyObject *)__pyx_n_s__i)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i)); __Pyx_INCREF(((PyObject *)__pyx_n_s__s)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 4, ((PyObject *)__pyx_n_s__s)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 4, ((PyObject *)__pyx_n_s__s)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s)); __Pyx_INCREF(((PyObject *)__pyx_n_s__err)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 5, ((PyObject *)__pyx_n_s__err)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 5, ((PyObject *)__pyx_n_s__err)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__err)); __Pyx_INCREF(((PyObject *)__pyx_n_s__x)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 6, ((PyObject *)__pyx_n_s__x)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 6, ((PyObject *)__pyx_n_s__x)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__x)); __Pyx_INCREF(((PyObject *)__pyx_n_s__y)); - PyTuple_SET_ITEM(__pyx_k_tuple_194, 7, ((PyObject *)__pyx_n_s__y)); + PyTuple_SET_ITEM(__pyx_k_tuple_195, 7, ((PyObject *)__pyx_n_s__y)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__y)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_194)); - __pyx_k_codeobj_195 = (PyObject*)__Pyx_PyCode_New(2, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_194, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_heading, 553, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_195)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_195)); + __pyx_k_codeobj_196 = (PyObject*)__Pyx_PyCode_New(2, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_195, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_heading, 553, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_196)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":581 + /* "pysam/cvcf.pyx":581 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) * * def write_heading( self, stream ): # <<<<<<<<<<<<<< * stream.write("#" + "\t".join(self._required + self._samples) + "\n") * */ - __pyx_k_tuple_196 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_196)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_196); + __pyx_k_tuple_197 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_197)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_197); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_196, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_197, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_196, 1, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_197, 1, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_196)); - __pyx_k_codeobj_197 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_196, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_heading, 581, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_197)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_197)); + __pyx_k_codeobj_198 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_197, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_heading, 581, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_198)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":584 + /* "pysam/cvcf.pyx":584 * stream.write("#" + "\t".join(self._required + self._samples) + "\n") * * def convertGT(self, GTstring): # <<<<<<<<<<<<<< * if GTstring == ".": return ["."] * try: */ - __pyx_k_tuple_198 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_198)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_198); + __pyx_k_tuple_199 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_199)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_199); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_198, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_199, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__GTstring)); - PyTuple_SET_ITEM(__pyx_k_tuple_198, 1, ((PyObject *)__pyx_n_s__GTstring)); + PyTuple_SET_ITEM(__pyx_k_tuple_199, 1, ((PyObject *)__pyx_n_s__GTstring)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__GTstring)); __Pyx_INCREF(((PyObject *)__pyx_n_s__gts)); - PyTuple_SET_ITEM(__pyx_k_tuple_198, 2, ((PyObject *)__pyx_n_s__gts)); + PyTuple_SET_ITEM(__pyx_k_tuple_199, 2, ((PyObject *)__pyx_n_s__gts)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__gts)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_198)); - __pyx_k_codeobj_199 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_198, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGT, 584, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_199)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_199)); + __pyx_k_codeobj_200 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_199, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGT, 584, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_200)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":596 + /* "pysam/cvcf.pyx":596 * return [".","|","."] * * def convertGTback(self, GTdata): # <<<<<<<<<<<<<< * return ''.join(map(str,GTdata)) * */ - __pyx_k_tuple_200 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_200)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_200); + __pyx_k_tuple_201 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_201)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_201); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_200, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_201, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__GTdata)); - PyTuple_SET_ITEM(__pyx_k_tuple_200, 1, ((PyObject *)__pyx_n_s__GTdata)); + PyTuple_SET_ITEM(__pyx_k_tuple_201, 1, ((PyObject *)__pyx_n_s__GTdata)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__GTdata)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_200)); - __pyx_k_codeobj_201 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_200, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGTback, 596, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_201)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_201)); + __pyx_k_codeobj_202 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_201, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGTback, 596, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_202)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":599 + /* "pysam/cvcf.pyx":599 * return ''.join(map(str,GTdata)) * * def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<< * # To do: check that the right number of values is present * f = formatdict.get(key,None) */ - __pyx_k_tuple_202 = PyTuple_New(9); if (unlikely(!__pyx_k_tuple_202)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_202); + __pyx_k_tuple_203 = PyTuple_New(9); if (unlikely(!__pyx_k_tuple_203)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_203); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__key)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 1, ((PyObject *)__pyx_n_s__key)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 1, ((PyObject *)__pyx_n_s__key)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key)); __Pyx_INCREF(((PyObject *)__pyx_n_s__value)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 2, ((PyObject *)__pyx_n_s__value)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 2, ((PyObject *)__pyx_n_s__value)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value)); __Pyx_INCREF(((PyObject *)__pyx_n_s__formatdict)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 3, ((PyObject *)__pyx_n_s__formatdict)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 3, ((PyObject *)__pyx_n_s__formatdict)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__formatdict)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 4, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 4, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__f)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 5, ((PyObject *)__pyx_n_s__f)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 5, ((PyObject *)__pyx_n_s__f)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f)); __Pyx_INCREF(((PyObject *)__pyx_n_s__values)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 6, ((PyObject *)__pyx_n_s__values)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 6, ((PyObject *)__pyx_n_s__values)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__values)); __Pyx_INCREF(((PyObject *)__pyx_n_s__idx)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 7, ((PyObject *)__pyx_n_s__idx)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 7, ((PyObject *)__pyx_n_s__idx)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx)); __Pyx_INCREF(((PyObject *)__pyx_n_s__v)); - PyTuple_SET_ITEM(__pyx_k_tuple_202, 8, ((PyObject *)__pyx_n_s__v)); + PyTuple_SET_ITEM(__pyx_k_tuple_203, 8, ((PyObject *)__pyx_n_s__v)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_202)); - __pyx_k_codeobj_203 = (PyObject*)__Pyx_PyCode_New(5, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_202, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_formatdata, 599, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_203)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_203)); + __pyx_k_codeobj_204 = (PyObject*)__Pyx_PyCode_New(5, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_203, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_formatdata, 599, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_204)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":641 + /* "pysam/cvcf.pyx":641 * self.error(line,self.ERROR_INFO_STRING) * * def inregion(self, chrom, pos): # <<<<<<<<<<<<<< * if not self._regions: return True * for r in self._regions: */ - __pyx_k_tuple_204 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_204)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_204); + __pyx_k_tuple_205 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_205)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_205); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_204, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_205, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__chrom)); - PyTuple_SET_ITEM(__pyx_k_tuple_204, 1, ((PyObject *)__pyx_n_s__chrom)); + PyTuple_SET_ITEM(__pyx_k_tuple_205, 1, ((PyObject *)__pyx_n_s__chrom)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__chrom)); __Pyx_INCREF(((PyObject *)__pyx_n_s__pos)); - PyTuple_SET_ITEM(__pyx_k_tuple_204, 2, ((PyObject *)__pyx_n_s__pos)); + PyTuple_SET_ITEM(__pyx_k_tuple_205, 2, ((PyObject *)__pyx_n_s__pos)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos)); __Pyx_INCREF(((PyObject *)__pyx_n_s__r)); - PyTuple_SET_ITEM(__pyx_k_tuple_204, 3, ((PyObject *)__pyx_n_s__r)); + PyTuple_SET_ITEM(__pyx_k_tuple_205, 3, ((PyObject *)__pyx_n_s__r)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_204)); - __pyx_k_codeobj_205 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_204, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__inregion, 641, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_205)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_205)); + __pyx_k_codeobj_206 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_205, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__inregion, 641, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_206)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":647 + /* "pysam/cvcf.pyx":647 * return False * * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< * cols = line.split('\t') * if len(cols) != len(self._samples)+9: */ - __pyx_k_tuple_206 = PyTuple_New(45); if (unlikely(!__pyx_k_tuple_206)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_206); + __pyx_k_tuple_207 = PyTuple_New(45); if (unlikely(!__pyx_k_tuple_207)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_207); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 1, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 1, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__lineparse)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 2, ((PyObject *)__pyx_n_s__lineparse)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 2, ((PyObject *)__pyx_n_s__lineparse)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__lineparse)); __Pyx_INCREF(((PyObject *)__pyx_n_s__cols)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 3, ((PyObject *)__pyx_n_s__cols)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 3, ((PyObject *)__pyx_n_s__cols)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cols)); __Pyx_INCREF(((PyObject *)__pyx_n_s__chrom)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 4, ((PyObject *)__pyx_n_s__chrom)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 4, ((PyObject *)__pyx_n_s__chrom)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__chrom)); __Pyx_INCREF(((PyObject *)__pyx_n_s__pos)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 5, ((PyObject *)__pyx_n_s__pos)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 5, ((PyObject *)__pyx_n_s__pos)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos)); __Pyx_INCREF(((PyObject *)__pyx_n_s__id)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 6, ((PyObject *)__pyx_n_s__id)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 6, ((PyObject *)__pyx_n_s__id)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__id)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ref)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 7, ((PyObject *)__pyx_n_s__ref)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 7, ((PyObject *)__pyx_n_s__ref)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref)); __Pyx_INCREF(((PyObject *)__pyx_n_s__c)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 8, ((PyObject *)__pyx_n_s__c)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 8, ((PyObject *)__pyx_n_s__c)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__c)); __Pyx_INCREF(((PyObject *)__pyx_n_s__left)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 9, ((PyObject *)__pyx_n_s__left)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 9, ((PyObject *)__pyx_n_s__left)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__left)); __Pyx_INCREF(((PyObject *)__pyx_n_s__faref_leftflank)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 10, ((PyObject *)__pyx_n_s__faref_leftflank)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 10, ((PyObject *)__pyx_n_s__faref_leftflank)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__faref_leftflank)); __Pyx_INCREF(((PyObject *)__pyx_n_s__faref)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 11, ((PyObject *)__pyx_n_s__faref)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 11, ((PyObject *)__pyx_n_s__faref)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__faref)); __Pyx_INCREF(((PyObject *)__pyx_n_s__alt)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 12, ((PyObject *)__pyx_n_s__alt)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 12, ((PyObject *)__pyx_n_s__alt)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt)); __Pyx_INCREF(((PyObject *)__pyx_n_s__qual)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 13, ((PyObject *)__pyx_n_s__qual)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 13, ((PyObject *)__pyx_n_s__qual)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qual)); __Pyx_INCREF(((PyObject *)__pyx_n_s__filter)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 14, ((PyObject *)__pyx_n_s__filter)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 14, ((PyObject *)__pyx_n_s__filter)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter)); __Pyx_INCREF(((PyObject *)__pyx_n_s__info)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 15, ((PyObject *)__pyx_n_s__info)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 15, ((PyObject *)__pyx_n_s__info)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__info)); __Pyx_INCREF(((PyObject *)__pyx_n_s__blurp)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 16, ((PyObject *)__pyx_n_s__blurp)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 16, ((PyObject *)__pyx_n_s__blurp)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__blurp)); __Pyx_INCREF(((PyObject *)__pyx_n_s__elts)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 17, ((PyObject *)__pyx_n_s__elts)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 17, ((PyObject *)__pyx_n_s__elts)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts)); __Pyx_INCREF(((PyObject *)__pyx_n_s__v)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 18, ((PyObject *)__pyx_n_s__v)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 18, ((PyObject *)__pyx_n_s__v)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v)); __Pyx_INCREF(((PyObject *)__pyx_n_s__format)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 19, ((PyObject *)__pyx_n_s__format)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 19, ((PyObject *)__pyx_n_s__format)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format)); __Pyx_INCREF(((PyObject *)__pyx_n_s__f)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 20, ((PyObject *)__pyx_n_s__f)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 20, ((PyObject *)__pyx_n_s__f)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f)); __Pyx_INCREF(((PyObject *)__pyx_n_s__newalts)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 21, ((PyObject *)__pyx_n_s__newalts)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 21, ((PyObject *)__pyx_n_s__newalts)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__newalts)); __Pyx_INCREF(((PyObject *)__pyx_n_s__have_deletions)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 22, ((PyObject *)__pyx_n_s__have_deletions)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 22, ((PyObject *)__pyx_n_s__have_deletions)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__have_deletions)); __Pyx_INCREF(((PyObject *)__pyx_n_s__a)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 23, ((PyObject *)__pyx_n_s__a)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 23, ((PyObject *)__pyx_n_s__a)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__a)); __Pyx_INCREF(((PyObject *)__pyx_n_s__l)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 24, ((PyObject *)__pyx_n_s__l)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 24, ((PyObject *)__pyx_n_s__l)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l)); __Pyx_INCREF(((PyObject *)__pyx_n_s__addns)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 25, ((PyObject *)__pyx_n_s__addns)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 25, ((PyObject *)__pyx_n_s__addns)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__addns)); __Pyx_INCREF(((PyObject *)__pyx_n_s__i)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 26, ((PyObject *)__pyx_n_s__i)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 26, ((PyObject *)__pyx_n_s__i)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i)); __Pyx_INCREF(((PyObject *)__pyx_n_s__na)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 27, ((PyObject *)__pyx_n_s__na)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 27, ((PyObject *)__pyx_n_s__na)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__na)); __Pyx_INCREF(((PyObject *)__pyx_n_s__s)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 28, ((PyObject *)__pyx_n_s__s)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 28, ((PyObject *)__pyx_n_s__s)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s)); __Pyx_INCREF(((PyObject *)__pyx_n_s__addn)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 29, ((PyObject *)__pyx_n_s__addn)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 29, ((PyObject *)__pyx_n_s__addn)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__addn)); __Pyx_INCREF(((PyObject *)__pyx_n_s__allele)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 30, ((PyObject *)__pyx_n_s__allele)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 30, ((PyObject *)__pyx_n_s__allele)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__allele)); __Pyx_INCREF(((PyObject *)__pyx_n_s__movable)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 31, ((PyObject *)__pyx_n_s__movable)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 31, ((PyObject *)__pyx_n_s__movable)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__movable)); __Pyx_INCREF(((PyObject *)__pyx_n_s__longest)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 32, ((PyObject *)__pyx_n_s__longest)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 32, ((PyObject *)__pyx_n_s__longest)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__longest)); __Pyx_INCREF(((PyObject *)__pyx_n_s__shortest)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 33, ((PyObject *)__pyx_n_s__shortest)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 33, ((PyObject *)__pyx_n_s__shortest)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__shortest)); __Pyx_INCREF(((PyObject *)__pyx_n_s__samples)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 34, ((PyObject *)__pyx_n_s__samples)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 34, ((PyObject *)__pyx_n_s__samples)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__samples)); __Pyx_INCREF(((PyObject *)__pyx_n_s__sample)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 35, ((PyObject *)__pyx_n_s__sample)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 35, ((PyObject *)__pyx_n_s__sample)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__sample)); __Pyx_INCREF(((PyObject *)__pyx_n_s__dict)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 36, ((PyObject *)__pyx_n_s__dict)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 36, ((PyObject *)__pyx_n_s__dict)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__dict)); __Pyx_INCREF(((PyObject *)__pyx_n_s__values)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 37, ((PyObject *)__pyx_n_s__values)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 37, ((PyObject *)__pyx_n_s__values)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__values)); __Pyx_INCREF(((PyObject *)__pyx_n_s__idx)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 38, ((PyObject *)__pyx_n_s__idx)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 38, ((PyObject *)__pyx_n_s__idx)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx)); __Pyx_INCREF(((PyObject *)__pyx_n_s__expected)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 39, ((PyObject *)__pyx_n_s__expected)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 39, ((PyObject *)__pyx_n_s__expected)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__expected)); __Pyx_INCREF(((PyObject *)__pyx_n_s__value)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 40, ((PyObject *)__pyx_n_s__value)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 40, ((PyObject *)__pyx_n_s__value)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value)); __Pyx_INCREF(((PyObject *)__pyx_n_s__d)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 41, ((PyObject *)__pyx_n_s__d)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 41, ((PyObject *)__pyx_n_s__d)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__d)); __Pyx_INCREF(((PyObject *)__pyx_n_s__key)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 42, ((PyObject *)__pyx_n_s__key)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 42, ((PyObject *)__pyx_n_s__key)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key)); __Pyx_INCREF(((PyObject *)__pyx_n_s__genexpr)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 43, ((PyObject *)__pyx_n_s__genexpr)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 43, ((PyObject *)__pyx_n_s__genexpr)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__genexpr)); __Pyx_INCREF(((PyObject *)__pyx_n_s__genexpr)); - PyTuple_SET_ITEM(__pyx_k_tuple_206, 44, ((PyObject *)__pyx_n_s__genexpr)); + PyTuple_SET_ITEM(__pyx_k_tuple_207, 44, ((PyObject *)__pyx_n_s__genexpr)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__genexpr)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_206)); - __pyx_k_codeobj_207 = (PyObject*)__Pyx_PyCode_New(3, 0, 45, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_206, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_data, 647, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_207)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_207)); + __pyx_k_codeobj_208 = (PyObject*)__Pyx_PyCode_New(3, 0, 45, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_207, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_data, 647, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_208)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":857 + /* "pysam/cvcf.pyx":857 * * * def write_data(self, stream, data): # <<<<<<<<<<<<<< * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples * for k in required: */ - __pyx_k_tuple_208 = PyTuple_New(10); if (unlikely(!__pyx_k_tuple_208)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_208); + __pyx_k_tuple_209 = PyTuple_New(10); if (unlikely(!__pyx_k_tuple_209)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_209); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 1, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 1, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); __Pyx_INCREF(((PyObject *)__pyx_n_s__data)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 2, ((PyObject *)__pyx_n_s__data)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 2, ((PyObject *)__pyx_n_s__data)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data)); __Pyx_INCREF(((PyObject *)__pyx_n_s__required)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 3, ((PyObject *)__pyx_n_s__required)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 3, ((PyObject *)__pyx_n_s__required)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__required)); __Pyx_INCREF(((PyObject *)__pyx_n_s__k)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 4, ((PyObject *)__pyx_n_s__k)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 4, ((PyObject *)__pyx_n_s__k)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__k)); __Pyx_INCREF(((PyObject *)__pyx_n_s__alt)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 5, ((PyObject *)__pyx_n_s__alt)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 5, ((PyObject *)__pyx_n_s__alt)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt)); __Pyx_INCREF(((PyObject *)__pyx_n_s__filter)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 6, ((PyObject *)__pyx_n_s__filter)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 6, ((PyObject *)__pyx_n_s__filter)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter)); __Pyx_INCREF(((PyObject *)__pyx_n_s__qual)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 7, ((PyObject *)__pyx_n_s__qual)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 7, ((PyObject *)__pyx_n_s__qual)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qual)); __Pyx_INCREF(((PyObject *)__pyx_n_s__output)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 8, ((PyObject *)__pyx_n_s__output)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 8, ((PyObject *)__pyx_n_s__output)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__output)); __Pyx_INCREF(((PyObject *)__pyx_n_s__s)); - PyTuple_SET_ITEM(__pyx_k_tuple_208, 9, ((PyObject *)__pyx_n_s__s)); + PyTuple_SET_ITEM(__pyx_k_tuple_209, 9, ((PyObject *)__pyx_n_s__s)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_208)); - __pyx_k_codeobj_209 = (PyObject*)__Pyx_PyCode_New(3, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_208, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_data, 857, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_209)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_209)); + __pyx_k_codeobj_210 = (PyObject*)__Pyx_PyCode_New(3, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_209, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_data, 857, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_210)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":886 + /* "pysam/cvcf.pyx":886 * stream.write( "\t".join(output) + "\n" ) * * def _parse_header(self, stream): # <<<<<<<<<<<<<< * self._lineno = 0 * for line in stream: */ - __pyx_k_tuple_210 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_210)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_210); + __pyx_k_tuple_211 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_211)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_211); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_210, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_211, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_210, 1, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_211, 1, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_210, 2, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_211, 2, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_210)); - __pyx_k_codeobj_211 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_210, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse_header, 886, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_211)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_211)); + __pyx_k_codeobj_212 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_211, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse_header, 886, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_212)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":899 + /* "pysam/cvcf.pyx":899 * return line * * def _parse(self, line, stream): # <<<<<<<<<<<<<< * # deal with files with header only * if line.startswith("##"): return */ - __pyx_k_tuple_212 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_212)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_212); + __pyx_k_tuple_213 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_213)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_213); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_212, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_213, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__line)); - PyTuple_SET_ITEM(__pyx_k_tuple_212, 1, ((PyObject *)__pyx_n_s__line)); + PyTuple_SET_ITEM(__pyx_k_tuple_213, 1, ((PyObject *)__pyx_n_s__line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_212, 2, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_213, 2, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); __Pyx_INCREF(((PyObject *)__pyx_n_s__d)); - PyTuple_SET_ITEM(__pyx_k_tuple_212, 3, ((PyObject *)__pyx_n_s__d)); + PyTuple_SET_ITEM(__pyx_k_tuple_213, 3, ((PyObject *)__pyx_n_s__d)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__d)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_212)); - __pyx_k_codeobj_213 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_212, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse, 899, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_213)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_213)); + __pyx_k_codeobj_214 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_213, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse, 899, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_214)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":917 + /* "pysam/cvcf.pyx":917 * ###################################################################################################### * * def getsamples(self): # <<<<<<<<<<<<<< * """ List of samples in VCF file """ * return self._samples */ - __pyx_k_tuple_214 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_214)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_214); + __pyx_k_tuple_215 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_215)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_215); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_214, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_215, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_214)); - __pyx_k_codeobj_215 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_214, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getsamples, 917, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_215)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_215)); + __pyx_k_codeobj_216 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_215, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getsamples, 917, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_216)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":921 + /* "pysam/cvcf.pyx":921 * return self._samples * * def setsamples(self,samples): # <<<<<<<<<<<<<< * """ List of samples in VCF file """ * self._samples = samples */ - __pyx_k_tuple_216 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_216)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_216); + __pyx_k_tuple_217 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_217)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_217); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_216, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_217, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__samples)); - PyTuple_SET_ITEM(__pyx_k_tuple_216, 1, ((PyObject *)__pyx_n_s__samples)); + PyTuple_SET_ITEM(__pyx_k_tuple_217, 1, ((PyObject *)__pyx_n_s__samples)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__samples)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_216)); - __pyx_k_codeobj_217 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_216, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setsamples, 921, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_217)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_217)); + __pyx_k_codeobj_218 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_217, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setsamples, 921, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_218)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":925 + /* "pysam/cvcf.pyx":925 * self._samples = samples * * def getheader(self): # <<<<<<<<<<<<<< * """ List of header key-value pairs (strings) """ * return self._header */ - __pyx_k_tuple_218 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_218)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_218); + __pyx_k_tuple_219 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_219)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_219); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_218, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_219, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_218)); - __pyx_k_codeobj_219 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_218, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getheader, 925, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_219)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_219)); + __pyx_k_codeobj_220 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_219, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getheader, 925, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_220)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":929 + /* "pysam/cvcf.pyx":929 * return self._header * * def setheader(self,header): # <<<<<<<<<<<<<< * """ List of header key-value pairs (strings) """ * self._header = header */ - __pyx_k_tuple_220 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_220)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_220); + __pyx_k_tuple_221 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_221)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_221); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_220, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_221, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__header)); - PyTuple_SET_ITEM(__pyx_k_tuple_220, 1, ((PyObject *)__pyx_n_s__header)); + PyTuple_SET_ITEM(__pyx_k_tuple_221, 1, ((PyObject *)__pyx_n_s__header)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__header)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_220)); - __pyx_k_codeobj_221 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_220, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setheader, 929, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_221)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_221)); + __pyx_k_codeobj_222 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_221, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setheader, 929, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_222)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":933 + /* "pysam/cvcf.pyx":933 * self._header = header * * def getinfo(self): # <<<<<<<<<<<<<< * """ Dictionary of ##INFO tags, as VCF.FORMAT values """ * return self._info */ - __pyx_k_tuple_222 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_222)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_222); + __pyx_k_tuple_223 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_223)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_223); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_222, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_223, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_222)); - __pyx_k_codeobj_223 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_222, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getinfo, 933, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_223)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_223)); + __pyx_k_codeobj_224 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_223, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getinfo, 933, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_224)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":937 + /* "pysam/cvcf.pyx":937 * return self._info * * def setinfo(self,info): # <<<<<<<<<<<<<< * """ Dictionary of ##INFO tags, as VCF.FORMAT values """ * self._info = info */ - __pyx_k_tuple_224 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_224)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_224); + __pyx_k_tuple_225 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_225)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_225); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_224, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_225, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__info)); - PyTuple_SET_ITEM(__pyx_k_tuple_224, 1, ((PyObject *)__pyx_n_s__info)); + PyTuple_SET_ITEM(__pyx_k_tuple_225, 1, ((PyObject *)__pyx_n_s__info)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__info)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_224)); - __pyx_k_codeobj_225 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_224, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setinfo, 937, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_225)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_225)); + __pyx_k_codeobj_226 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_225, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setinfo, 937, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_226)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":941 + /* "pysam/cvcf.pyx":941 * self._info = info * * def getformat(self): # <<<<<<<<<<<<<< * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * return self._format */ - __pyx_k_tuple_226 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_226)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_226); + __pyx_k_tuple_227 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_227)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_227); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_226, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_227, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_226)); - __pyx_k_codeobj_227 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_226, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getformat, 941, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_227)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_227)); + __pyx_k_codeobj_228 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_227, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getformat, 941, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_228)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":945 + /* "pysam/cvcf.pyx":945 * return self._format * * def setformat(self,format): # <<<<<<<<<<<<<< * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * self._format = format */ - __pyx_k_tuple_228 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_228)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_228); + __pyx_k_tuple_229 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_229)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_229); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_228, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_229, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__format)); - PyTuple_SET_ITEM(__pyx_k_tuple_228, 1, ((PyObject *)__pyx_n_s__format)); + PyTuple_SET_ITEM(__pyx_k_tuple_229, 1, ((PyObject *)__pyx_n_s__format)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_228)); - __pyx_k_codeobj_229 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_228, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setformat, 945, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_229)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_229)); + __pyx_k_codeobj_230 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_229, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setformat, 945, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_230)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":949 + /* "pysam/cvcf.pyx":949 * self._format = format * * def getfilter(self): # <<<<<<<<<<<<<< * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * return self._filter */ - __pyx_k_tuple_230 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_230)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_230); + __pyx_k_tuple_231 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_231)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_231); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_230, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_231, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_230)); - __pyx_k_codeobj_231 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_230, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getfilter, 949, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_231)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_231)); + __pyx_k_codeobj_232 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_231, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getfilter, 949, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_232)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":953 + /* "pysam/cvcf.pyx":953 * return self._filter * * def setfilter(self,filter): # <<<<<<<<<<<<<< * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * self._filter = filter */ - __pyx_k_tuple_232 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_232)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_232); + __pyx_k_tuple_233 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_233)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_233); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_232, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_233, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__filter)); - PyTuple_SET_ITEM(__pyx_k_tuple_232, 1, ((PyObject *)__pyx_n_s__filter)); + PyTuple_SET_ITEM(__pyx_k_tuple_233, 1, ((PyObject *)__pyx_n_s__filter)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_232)); - __pyx_k_codeobj_233 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_232, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setfilter, 953, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_233)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_233)); + __pyx_k_codeobj_234 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_233, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setfilter, 953, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_234)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":957 + /* "pysam/cvcf.pyx":957 * self._filter = filter * * def setversion(self, version): # <<<<<<<<<<<<<< * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") * self._version = version */ - __pyx_k_tuple_234 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_234)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_234); + __pyx_k_tuple_235 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_235)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_235); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_234, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_235, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__version)); - PyTuple_SET_ITEM(__pyx_k_tuple_234, 1, ((PyObject *)__pyx_n_s__version)); + PyTuple_SET_ITEM(__pyx_k_tuple_235, 1, ((PyObject *)__pyx_n_s__version)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__version)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_234)); - __pyx_k_codeobj_235 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_234, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setversion, 957, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_235)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_235)); + __pyx_k_codeobj_236 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_235, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setversion, 957, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_236)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":961 + /* "pysam/cvcf.pyx":961 * self._version = version * * def setregions(self, regions): # <<<<<<<<<<<<<< * self._regions = regions * */ - __pyx_k_tuple_236 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_236)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_236); + __pyx_k_tuple_237 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_237)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_237); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_236, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_237, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__regions)); - PyTuple_SET_ITEM(__pyx_k_tuple_236, 1, ((PyObject *)__pyx_n_s__regions)); + PyTuple_SET_ITEM(__pyx_k_tuple_237, 1, ((PyObject *)__pyx_n_s__regions)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__regions)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_236)); - __pyx_k_codeobj_237 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_236, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setregions, 961, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_237)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_237)); + __pyx_k_codeobj_238 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_237, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setregions, 961, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_238)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":964 + /* "pysam/cvcf.pyx":964 * self._regions = regions * * def setreference(self, ref): # <<<<<<<<<<<<<< * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """ * self._reference = ref */ - __pyx_k_tuple_238 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_238)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_238); + __pyx_k_tuple_239 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_239)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_239); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_238, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_239, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ref)); - PyTuple_SET_ITEM(__pyx_k_tuple_238, 1, ((PyObject *)__pyx_n_s__ref)); + PyTuple_SET_ITEM(__pyx_k_tuple_239, 1, ((PyObject *)__pyx_n_s__ref)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_238)); - __pyx_k_codeobj_239 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_238, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setreference, 964, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_239)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_239)); + __pyx_k_codeobj_240 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_239, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setreference, 964, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_240)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":968 + /* "pysam/cvcf.pyx":968 * self._reference = ref * * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<< * try: self._ignored_errors.add(self.__dict__[errorstring]) * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ - __pyx_k_tuple_240 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_240)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_240); + __pyx_k_tuple_241 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_241)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_241); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_240, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_241, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__errorstring)); - PyTuple_SET_ITEM(__pyx_k_tuple_240, 1, ((PyObject *)__pyx_n_s__errorstring)); + PyTuple_SET_ITEM(__pyx_k_tuple_241, 1, ((PyObject *)__pyx_n_s__errorstring)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorstring)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_240)); - __pyx_k_codeobj_241 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_240, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__ignoreerror, 968, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_241)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_241)); + __pyx_k_codeobj_242 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_241, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__ignoreerror, 968, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_242)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":972 + /* "pysam/cvcf.pyx":972 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) * * def warnerror(self, errorstring): # <<<<<<<<<<<<<< * try: self._warn_errors.add(self.__dict__[errorstring]) * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ - __pyx_k_tuple_242 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_242)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_242); + __pyx_k_tuple_243 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_243)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_243); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_242, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_243, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__errorstring)); - PyTuple_SET_ITEM(__pyx_k_tuple_242, 1, ((PyObject *)__pyx_n_s__errorstring)); + PyTuple_SET_ITEM(__pyx_k_tuple_243, 1, ((PyObject *)__pyx_n_s__errorstring)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorstring)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_242)); - __pyx_k_codeobj_243 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_242, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__warnerror, 972, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_243)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_243)); + __pyx_k_codeobj_244 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_243, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__warnerror, 972, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_244)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":976 + /* "pysam/cvcf.pyx":976 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) * * def parse(self, stream): # <<<<<<<<<<<<<< * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ * last_line = self._parse_header(stream) */ - __pyx_k_tuple_244 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_244)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_244); + __pyx_k_tuple_245 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_245)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_245); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_244, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_245, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_244, 1, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_245, 1, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); __Pyx_INCREF(((PyObject *)__pyx_n_s__last_line)); - PyTuple_SET_ITEM(__pyx_k_tuple_244, 2, ((PyObject *)__pyx_n_s__last_line)); + PyTuple_SET_ITEM(__pyx_k_tuple_245, 2, ((PyObject *)__pyx_n_s__last_line)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__last_line)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_244)); - __pyx_k_codeobj_245 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_244, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse, 976, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_245)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_245)); + __pyx_k_codeobj_246 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_245, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse, 976, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_246)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":983 + /* "pysam/cvcf.pyx":983 * return self._parse(last_line, stream) * * def write(self, stream, datagenerator): # <<<<<<<<<<<<<< * """ Writes a VCF file to a stream, using a data generator (or list) """ * self.write_header(stream) */ - __pyx_k_tuple_246 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_246)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_246); + __pyx_k_tuple_247 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_247)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_247); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_246, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_247, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_246, 1, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_247, 1, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); __Pyx_INCREF(((PyObject *)__pyx_n_s__datagenerator)); - PyTuple_SET_ITEM(__pyx_k_tuple_246, 2, ((PyObject *)__pyx_n_s__datagenerator)); + PyTuple_SET_ITEM(__pyx_k_tuple_247, 2, ((PyObject *)__pyx_n_s__datagenerator)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__datagenerator)); __Pyx_INCREF(((PyObject *)__pyx_n_s__data)); - PyTuple_SET_ITEM(__pyx_k_tuple_246, 3, ((PyObject *)__pyx_n_s__data)); + PyTuple_SET_ITEM(__pyx_k_tuple_247, 3, ((PyObject *)__pyx_n_s__data)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_246)); - __pyx_k_codeobj_247 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_246, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write, 983, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_247)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_247)); + __pyx_k_codeobj_248 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_247, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write, 983, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_248)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":989 + /* "pysam/cvcf.pyx":989 * for data in datagenerator: self.write_data(stream,data) * * def writeheader(self, stream): # <<<<<<<<<<<<<< * """ Writes a VCF header """ * self.write_header(stream) */ - __pyx_k_tuple_248 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_248)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_248); + __pyx_k_tuple_249 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_249)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_249); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_248, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_249, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__stream)); - PyTuple_SET_ITEM(__pyx_k_tuple_248, 1, ((PyObject *)__pyx_n_s__stream)); + PyTuple_SET_ITEM(__pyx_k_tuple_249, 1, ((PyObject *)__pyx_n_s__stream)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_248)); - __pyx_k_codeobj_249 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_248, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__writeheader, 989, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_249)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_249)); + __pyx_k_codeobj_250 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_249, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__writeheader, 989, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_250)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":994 + /* "pysam/cvcf.pyx":994 * self.write_heading(stream) * * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<< * """ Utility function: compares two calls for equality """ * # a variant should always be assigned to a unique position, one base before */ - __pyx_k_tuple_250 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_250)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_250); + __pyx_k_tuple_251 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_251)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_251); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_250, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_251, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__pos1)); - PyTuple_SET_ITEM(__pyx_k_tuple_250, 1, ((PyObject *)__pyx_n_s__pos1)); + PyTuple_SET_ITEM(__pyx_k_tuple_251, 1, ((PyObject *)__pyx_n_s__pos1)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos1)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ref1)); - PyTuple_SET_ITEM(__pyx_k_tuple_250, 2, ((PyObject *)__pyx_n_s__ref1)); + PyTuple_SET_ITEM(__pyx_k_tuple_251, 2, ((PyObject *)__pyx_n_s__ref1)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref1)); __Pyx_INCREF(((PyObject *)__pyx_n_s__alt1)); - PyTuple_SET_ITEM(__pyx_k_tuple_250, 3, ((PyObject *)__pyx_n_s__alt1)); + PyTuple_SET_ITEM(__pyx_k_tuple_251, 3, ((PyObject *)__pyx_n_s__alt1)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt1)); __Pyx_INCREF(((PyObject *)__pyx_n_s__pos2)); - PyTuple_SET_ITEM(__pyx_k_tuple_250, 4, ((PyObject *)__pyx_n_s__pos2)); + PyTuple_SET_ITEM(__pyx_k_tuple_251, 4, ((PyObject *)__pyx_n_s__pos2)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos2)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ref2)); - PyTuple_SET_ITEM(__pyx_k_tuple_250, 5, ((PyObject *)__pyx_n_s__ref2)); + PyTuple_SET_ITEM(__pyx_k_tuple_251, 5, ((PyObject *)__pyx_n_s__ref2)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref2)); __Pyx_INCREF(((PyObject *)__pyx_n_s__alt2)); - PyTuple_SET_ITEM(__pyx_k_tuple_250, 6, ((PyObject *)__pyx_n_s__alt2)); + PyTuple_SET_ITEM(__pyx_k_tuple_251, 6, ((PyObject *)__pyx_n_s__alt2)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt2)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_250)); - __pyx_k_codeobj_251 = (PyObject*)__Pyx_PyCode_New(7, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_250, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__compare_calls, 994, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_251)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_251)); + __pyx_k_codeobj_252 = (PyObject*)__Pyx_PyCode_New(7, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_251, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__compare_calls, 994, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_252)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":1016 + /* "pysam/cvcf.pyx":1016 * ########################################################################################################### * * def connect( self, filename ): # <<<<<<<<<<<<<< * '''connect to tabix file.''' * self.tabixfile = pysam.Tabixfile( filename ) */ - __pyx_k_tuple_252 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_252)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_252); + __pyx_k_tuple_253 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_253)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_253); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_252, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_253, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__filename)); - PyTuple_SET_ITEM(__pyx_k_tuple_252, 1, ((PyObject *)__pyx_n_s__filename)); + PyTuple_SET_ITEM(__pyx_k_tuple_253, 1, ((PyObject *)__pyx_n_s__filename)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_252)); - __pyx_k_codeobj_253 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_252, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__connect, 1016, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_253)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_253)); + __pyx_k_codeobj_254 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_253, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__connect, 1016, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_254)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":1021 + /* "pysam/cvcf.pyx":1021 * self._parse_header(self.tabixfile.header) * * def fetch(self, # <<<<<<<<<<<<<< * reference = None, * start = None, */ - __pyx_k_tuple_254 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_254)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_254); + __pyx_k_tuple_255 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_255); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_254, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_255, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__reference)); - PyTuple_SET_ITEM(__pyx_k_tuple_254, 1, ((PyObject *)__pyx_n_s__reference)); + PyTuple_SET_ITEM(__pyx_k_tuple_255, 1, ((PyObject *)__pyx_n_s__reference)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__reference)); __Pyx_INCREF(((PyObject *)__pyx_n_s__start)); - PyTuple_SET_ITEM(__pyx_k_tuple_254, 2, ((PyObject *)__pyx_n_s__start)); + PyTuple_SET_ITEM(__pyx_k_tuple_255, 2, ((PyObject *)__pyx_n_s__start)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__start)); __Pyx_INCREF(((PyObject *)__pyx_n_s__end)); - PyTuple_SET_ITEM(__pyx_k_tuple_254, 3, ((PyObject *)__pyx_n_s__end)); + PyTuple_SET_ITEM(__pyx_k_tuple_255, 3, ((PyObject *)__pyx_n_s__end)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__end)); __Pyx_INCREF(((PyObject *)__pyx_n_s__region)); - PyTuple_SET_ITEM(__pyx_k_tuple_254, 4, ((PyObject *)__pyx_n_s__region)); + PyTuple_SET_ITEM(__pyx_k_tuple_255, 4, ((PyObject *)__pyx_n_s__region)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__region)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_254)); - __pyx_k_codeobj_255 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_254, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__fetch, 1021, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_k_tuple_256 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_256)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_256); + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_255)); + __pyx_k_codeobj_256 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_255, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__fetch, 1021, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_256)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_k_tuple_257 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_257)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_257); __Pyx_INCREF(((PyObject *)Py_None)); - PyTuple_SET_ITEM(__pyx_k_tuple_256, 0, ((PyObject *)Py_None)); + PyTuple_SET_ITEM(__pyx_k_tuple_257, 0, ((PyObject *)Py_None)); __Pyx_GIVEREF(((PyObject *)Py_None)); __Pyx_INCREF(((PyObject *)Py_None)); - PyTuple_SET_ITEM(__pyx_k_tuple_256, 1, ((PyObject *)Py_None)); + PyTuple_SET_ITEM(__pyx_k_tuple_257, 1, ((PyObject *)Py_None)); __Pyx_GIVEREF(((PyObject *)Py_None)); __Pyx_INCREF(((PyObject *)Py_None)); - PyTuple_SET_ITEM(__pyx_k_tuple_256, 2, ((PyObject *)Py_None)); + PyTuple_SET_ITEM(__pyx_k_tuple_257, 2, ((PyObject *)Py_None)); __Pyx_GIVEREF(((PyObject *)Py_None)); __Pyx_INCREF(((PyObject *)Py_None)); - PyTuple_SET_ITEM(__pyx_k_tuple_256, 3, ((PyObject *)Py_None)); + PyTuple_SET_ITEM(__pyx_k_tuple_257, 3, ((PyObject *)Py_None)); __Pyx_GIVEREF(((PyObject *)Py_None)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_256)); + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_257)); - /* "cvcf.pyx":1030 + /* "pysam/cvcf.pyx":1030 * return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) ) * * def validate( self, record ): # <<<<<<<<<<<<<< * '''validate vcf record. * */ - __pyx_k_tuple_257 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_257)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_257); + __pyx_k_tuple_258 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_k_tuple_258); __Pyx_INCREF(((PyObject *)__pyx_n_s__self)); - PyTuple_SET_ITEM(__pyx_k_tuple_257, 0, ((PyObject *)__pyx_n_s__self)); + PyTuple_SET_ITEM(__pyx_k_tuple_258, 0, ((PyObject *)__pyx_n_s__self)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self)); __Pyx_INCREF(((PyObject *)__pyx_n_s__record)); - PyTuple_SET_ITEM(__pyx_k_tuple_257, 1, ((PyObject *)__pyx_n_s__record)); + PyTuple_SET_ITEM(__pyx_k_tuple_258, 1, ((PyObject *)__pyx_n_s__record)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__record)); - __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_257)); - __pyx_k_codeobj_258 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_257, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__validate, 1030, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258)); + __pyx_k_codeobj_259 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_258, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__validate, 1030, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -26439,20 +26748,27 @@ PyMODINIT_FUNC PyInit_cvcf(void) #endif /*--- Module creation code ---*/ #if PY_MAJOR_VERSION < 3 - __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION); + __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); #else __pyx_m = PyModule_Create(&__pyx_moduledef); #endif - if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; - #if PY_MAJOR_VERSION < 3 - Py_INCREF(__pyx_m); + if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if PY_MAJOR_VERSION >= 3 + { + PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!PyDict_GetItemString(modules, "pysam.cvcf")) { + if (unlikely(PyDict_SetItemString(modules, "pysam.cvcf", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + } + #endif + __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_PYPY + Py_INCREF(__pyx_b); #endif - __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); - if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; /*--- Initialize various global constants etc. ---*/ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__pyx_module_is_main_cvcf) { + if (__pyx_module_is_main_pysam__cvcf) { if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; } /*--- Builtin init code ---*/ @@ -26463,53 +26779,53 @@ PyMODINIT_FUNC PyInit_cvcf(void) /*--- Variable export code ---*/ /*--- Function export code ---*/ /*--- Type init code ---*/ - __pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_4cvcf_VCFRecord = &__pyx_vtable_4cvcf_VCFRecord; - __pyx_vtable_4cvcf_VCFRecord.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy; - __pyx_vtable_4cvcf_VCFRecord.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_4cvcf_9VCFRecord_update; - __pyx_type_4cvcf_VCFRecord.tp_base = __pyx_ptype_10TabProxies_TupleProxy; - if (PyType_Ready(&__pyx_type_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetVtable(__pyx_type_4cvcf_VCFRecord.tp_dict, __pyx_vtabptr_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "VCFRecord", (PyObject *)&__pyx_type_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_4cvcf_VCFRecord = &__pyx_type_4cvcf_VCFRecord; - __pyx_ptype_6ctabix_Parser = __Pyx_ImportType("ctabix", "Parser", sizeof(struct __pyx_obj_6ctabix_Parser), 1); if (unlikely(!__pyx_ptype_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_type_4cvcf_asVCFRecord.tp_base = __pyx_ptype_6ctabix_Parser; - if (PyType_Ready(&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_4cvcf_asVCFRecord = &__pyx_type_4cvcf_asVCFRecord; - if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_4cvcf___pyx_scope_struct__parse_data = &__pyx_type_4cvcf___pyx_scope_struct__parse_data; - if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr = &__pyx_type_4cvcf___pyx_scope_struct_1_genexpr; - if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_4cvcf___pyx_scope_struct_2__parse = &__pyx_type_4cvcf___pyx_scope_struct_2__parse; + __pyx_ptype_5pysam_10TabProxies_TupleProxy = __Pyx_ImportType("pysam.TabProxies", "TupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_4cvcf_VCFRecord = &__pyx_vtable_5pysam_4cvcf_VCFRecord; + __pyx_vtable_5pysam_4cvcf_VCFRecord.__pyx_base = *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy; + __pyx_vtable_5pysam_4cvcf_VCFRecord.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_4cvcf_9VCFRecord_update; + __pyx_type_5pysam_4cvcf_VCFRecord.tp_base = __pyx_ptype_5pysam_10TabProxies_TupleProxy; + if (PyType_Ready(&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type_5pysam_4cvcf_VCFRecord.tp_dict, __pyx_vtabptr_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "VCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_4cvcf_VCFRecord = &__pyx_type_5pysam_4cvcf_VCFRecord; + __pyx_ptype_5pysam_6ctabix_Parser = __Pyx_ImportType("pysam.ctabix", "Parser", sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_5pysam_4cvcf_asVCFRecord.tp_base = __pyx_ptype_5pysam_6ctabix_Parser; + if (PyType_Ready(&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_4cvcf_asVCFRecord = &__pyx_type_5pysam_4cvcf_asVCFRecord; + if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data = &__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data; + if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr = &__pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr; + if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = &__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse; /*--- Type import code ---*/ - __pyx_ptype_6ctabix_Tabixfile = __Pyx_ImportType("ctabix", "Tabixfile", sizeof(struct __pyx_obj_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_TabixIterator = __Pyx_ImportType("ctabix", "TabixIterator", sizeof(struct __pyx_obj_6ctabix_TabixIterator), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_TabixHeaderIterator = __Pyx_ImportType("ctabix", "TabixHeaderIterator", sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixHeaderIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asTuple = __Pyx_ImportType("ctabix", "asTuple", sizeof(struct __pyx_obj_6ctabix_asTuple), 1); if (unlikely(!__pyx_ptype_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asGTF = __Pyx_ImportType("ctabix", "asGTF", sizeof(struct __pyx_obj_6ctabix_asGTF), 1); if (unlikely(!__pyx_ptype_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asBed = __Pyx_ImportType("ctabix", "asBed", sizeof(struct __pyx_obj_6ctabix_asBed), 1); if (unlikely(!__pyx_ptype_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_asVCF = __Pyx_ImportType("ctabix", "asVCF", sizeof(struct __pyx_obj_6ctabix_asVCF), 1); if (unlikely(!__pyx_ptype_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_TabixIteratorParsed = __Pyx_ImportType("ctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_6ctabix_TabixIteratorParsed), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixIteratorParsed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_tabix_inplace_iterator = __Pyx_ImportType("ctabix", "tabix_inplace_iterator", sizeof(struct __pyx_obj_6ctabix_tabix_inplace_iterator), 1); if (unlikely(!__pyx_ptype_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_6ctabix_tabix_inplace_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_inplace_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_6ctabix_tabix_copy_iterator = __Pyx_ImportType("ctabix", "tabix_copy_iterator", sizeof(struct __pyx_obj_6ctabix_tabix_copy_iterator), 1); if (unlikely(!__pyx_ptype_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_Tabixfile = __Pyx_ImportType("pysam.ctabix", "Tabixfile", sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_TabixIterator = __Pyx_ImportType("pysam.ctabix", "TabixIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = __Pyx_ImportType("pysam.ctabix", "TabixHeaderIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asTuple = __Pyx_ImportType("pysam.ctabix", "asTuple", sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asGTF = __Pyx_ImportType("pysam.ctabix", "asGTF", sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asBed = __Pyx_ImportType("pysam.ctabix", "asBed", sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_asVCF = __Pyx_ImportType("pysam.ctabix", "asVCF", sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = __Pyx_ImportType("pysam.ctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = __Pyx_ImportType("pysam.ctabix", "tabix_inplace_iterator", sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = (struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = __Pyx_ImportType("pysam.ctabix", "tabix_copy_iterator", sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_GTFProxy = __Pyx_ImportType("pysam.TabProxies", "GTFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = __Pyx_ImportType("pysam.TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_BedProxy = __Pyx_ImportType("pysam.TabProxies", "BedProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_BedProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5pysam_10TabProxies_VCFProxy = __Pyx_ImportType("pysam.TabProxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_5pysam_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ - /* "cvcf.pyx":46 + /* "pysam/cvcf.pyx":46 * # * * from collections import namedtuple, defaultdict # <<<<<<<<<<<<<< @@ -26545,7 +26861,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":47 + /* "pysam/cvcf.pyx":47 * * from collections import namedtuple, defaultdict * from operator import itemgetter # <<<<<<<<<<<<<< @@ -26570,12 +26886,12 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":48 + /* "pysam/cvcf.pyx":48 * from collections import namedtuple, defaultdict * from operator import itemgetter * import sys, re, copy, bisect # <<<<<<<<<<<<<< * - * cimport ctabix + * from pysam cimport ctabix */ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__sys), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -26594,9 +26910,9 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s__bisect, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":52 - * cimport ctabix - * cimport TabProxies + /* "pysam/cvcf.pyx":52 + * from pysam cimport ctabix + * from pysam cimport TabProxies * import pysam # <<<<<<<<<<<<<< * * gtsRegEx = re.compile("[|/\\\\]") @@ -26606,7 +26922,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s__pysam, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":54 + /* "pysam/cvcf.pyx":54 * import pysam * * gtsRegEx = re.compile("[|/\\\\]") # <<<<<<<<<<<<<< @@ -26624,7 +26940,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s__gtsRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":55 + /* "pysam/cvcf.pyx":55 * * gtsRegEx = re.compile("[|/\\\\]") * alleleRegEx = re.compile('^[ACGTN]+$') # <<<<<<<<<<<<<< @@ -26642,31 +26958,31 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s__alleleRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":58 + /* "pysam/cvcf.pyx":58 * * # Utility function. Uses 0-based coordinates * def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<< * # obtain sequence from .fa file, without truncation * if end<=start: return "" */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_4cvcf_1get_sequence, NULL, __pyx_n_s__cvcf); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_1get_sequence, NULL, __pyx_n_s_135); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__get_sequence, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":68 + /* "pysam/cvcf.pyx":68 * * # Utility function. Parses a region string * def parse_regions( string ): # <<<<<<<<<<<<<< * result = [] * for r in string.split(','): */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_4cvcf_3parse_regions, NULL, __pyx_n_s__cvcf); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3parse_regions, NULL, __pyx_n_s_135); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__parse_regions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":86 + /* "pysam/cvcf.pyx":86 * * * FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') # <<<<<<<<<<<<<< @@ -26675,13 +26991,13 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__namedtuple); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_138), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (PyObject_SetAttr(__pyx_m, __pyx_n_s__FORMAT, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - /* "cvcf.pyx":237 + /* "pysam/cvcf.pyx":237 * return r * * class VCF(object): # <<<<<<<<<<<<<< @@ -26691,7 +27007,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); - /* "cvcf.pyx":240 + /* "pysam/cvcf.pyx":240 * * # types * NT_UNKNOWN = 0 # <<<<<<<<<<<<<< @@ -26700,7 +27016,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_UNKNOWN, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":241 + /* "pysam/cvcf.pyx":241 * # types * NT_UNKNOWN = 0 * NT_NUMBER = 1 # <<<<<<<<<<<<<< @@ -26709,7 +27025,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NUMBER, __pyx_int_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":242 + /* "pysam/cvcf.pyx":242 * NT_UNKNOWN = 0 * NT_NUMBER = 1 * NT_ALLELES = 2 # <<<<<<<<<<<<<< @@ -26718,7 +27034,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_ALLELES, __pyx_int_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":243 + /* "pysam/cvcf.pyx":243 * NT_NUMBER = 1 * NT_ALLELES = 2 * NT_NR_ALLELES = 3 # <<<<<<<<<<<<<< @@ -26727,7 +27043,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NR_ALLELES, __pyx_int_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":244 + /* "pysam/cvcf.pyx":244 * NT_ALLELES = 2 * NT_NR_ALLELES = 3 * NT_GENOTYPES = 4 # <<<<<<<<<<<<<< @@ -26736,7 +27052,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_GENOTYPES, __pyx_int_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":245 + /* "pysam/cvcf.pyx":245 * NT_NR_ALLELES = 3 * NT_GENOTYPES = 4 * NT_PHASED_GENOTYPES = 5 # <<<<<<<<<<<<<< @@ -26745,7 +27061,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_PHASED_GENOTYPES, __pyx_int_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":247 + /* "pysam/cvcf.pyx":247 * NT_PHASED_GENOTYPES = 5 * * _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier", # <<<<<<<<<<<<<< @@ -26754,44 +27070,44 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - if (PyDict_SetItem(__pyx_t_1, __pyx_int_0, ((PyObject *)__pyx_kp_s_139)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_1, ((PyObject *)__pyx_kp_s_140)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_2, ((PyObject *)__pyx_kp_s_141)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_3, ((PyObject *)__pyx_kp_s_142)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_4, ((PyObject *)__pyx_kp_s_143)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_5, ((PyObject *)__pyx_kp_s_144)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_6, ((PyObject *)__pyx_kp_s_145)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_7, ((PyObject *)__pyx_kp_s_146)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_8, ((PyObject *)__pyx_kp_s_147)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_9, ((PyObject *)__pyx_kp_s_148)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_10, ((PyObject *)__pyx_kp_s_149)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_11, ((PyObject *)__pyx_kp_s_150)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_12, ((PyObject *)__pyx_kp_s_151)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_13, ((PyObject *)__pyx_kp_s_152)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_14, ((PyObject *)__pyx_kp_s_153)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_15, ((PyObject *)__pyx_kp_s_154)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_16, ((PyObject *)__pyx_kp_s_155)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_17, ((PyObject *)__pyx_kp_s_156)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_18, ((PyObject *)__pyx_kp_s_157)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_19, ((PyObject *)__pyx_kp_s_158)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_20, ((PyObject *)__pyx_kp_s_159)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_21, ((PyObject *)__pyx_kp_s_160)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_22, ((PyObject *)__pyx_kp_s_161)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_23, ((PyObject *)__pyx_kp_s_162)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_24, ((PyObject *)__pyx_kp_s_163)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_25, ((PyObject *)__pyx_kp_s_164)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_26, ((PyObject *)__pyx_kp_s_165)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_27, ((PyObject *)__pyx_kp_s_166)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_28, ((PyObject *)__pyx_kp_s_167)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_29, ((PyObject *)__pyx_kp_s_168)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_30, ((PyObject *)__pyx_kp_s_169)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_31, ((PyObject *)__pyx_kp_s_170)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_32, ((PyObject *)__pyx_kp_s_171)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (PyDict_SetItem(__pyx_t_1, __pyx_int_33, ((PyObject *)__pyx_kp_s_172)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_0, ((PyObject *)__pyx_kp_s_140)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_1, ((PyObject *)__pyx_kp_s_141)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_2, ((PyObject *)__pyx_kp_s_142)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_3, ((PyObject *)__pyx_kp_s_143)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_4, ((PyObject *)__pyx_kp_s_144)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_5, ((PyObject *)__pyx_kp_s_145)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_6, ((PyObject *)__pyx_kp_s_146)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_7, ((PyObject *)__pyx_kp_s_147)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_8, ((PyObject *)__pyx_kp_s_148)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_9, ((PyObject *)__pyx_kp_s_149)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_10, ((PyObject *)__pyx_kp_s_150)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_11, ((PyObject *)__pyx_kp_s_151)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_12, ((PyObject *)__pyx_kp_s_152)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_13, ((PyObject *)__pyx_kp_s_153)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_14, ((PyObject *)__pyx_kp_s_154)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_15, ((PyObject *)__pyx_kp_s_155)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_16, ((PyObject *)__pyx_kp_s_156)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_17, ((PyObject *)__pyx_kp_s_157)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_18, ((PyObject *)__pyx_kp_s_158)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_19, ((PyObject *)__pyx_kp_s_159)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_20, ((PyObject *)__pyx_kp_s_160)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_21, ((PyObject *)__pyx_kp_s_161)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_22, ((PyObject *)__pyx_kp_s_162)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_23, ((PyObject *)__pyx_kp_s_163)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_24, ((PyObject *)__pyx_kp_s_164)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_25, ((PyObject *)__pyx_kp_s_165)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_26, ((PyObject *)__pyx_kp_s_166)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_27, ((PyObject *)__pyx_kp_s_167)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_28, ((PyObject *)__pyx_kp_s_168)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_29, ((PyObject *)__pyx_kp_s_169)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_30, ((PyObject *)__pyx_kp_s_170)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_31, ((PyObject *)__pyx_kp_s_171)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_32, ((PyObject *)__pyx_kp_s_172)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_int_33, ((PyObject *)__pyx_kp_s_173)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":284 + /* "pysam/cvcf.pyx":284 * * # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields * _header = [] # <<<<<<<<<<<<<< @@ -26803,7 +27119,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___header, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":287 + /* "pysam/cvcf.pyx":287 * * # version number; 33=v3.3; 40=v4.0 * _version = 40 # <<<<<<<<<<<<<< @@ -26812,7 +27128,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___version, __pyx_int_40) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":290 + /* "pysam/cvcf.pyx":290 * * # info, filter and format data * _info = {} # <<<<<<<<<<<<<< @@ -26824,7 +27140,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___info, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":291 + /* "pysam/cvcf.pyx":291 * # info, filter and format data * _info = {} * _filter = {} # <<<<<<<<<<<<<< @@ -26836,7 +27152,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___filter, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":292 + /* "pysam/cvcf.pyx":292 * _info = {} * _filter = {} * _format = {} # <<<<<<<<<<<<<< @@ -26848,7 +27164,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___format, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":295 + /* "pysam/cvcf.pyx":295 * * # header; and required columns * _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] # <<<<<<<<<<<<<< @@ -26887,7 +27203,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___required, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 295; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":296 + /* "pysam/cvcf.pyx":296 * # header; and required columns * _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] * _samples = [] # <<<<<<<<<<<<<< @@ -26899,7 +27215,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___samples, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":299 + /* "pysam/cvcf.pyx":299 * * # control behaviour * _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD # <<<<<<<<<<<<<< @@ -26913,7 +27229,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___ignored_errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":300 + /* "pysam/cvcf.pyx":300 * # control behaviour * _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD * _warn_errors = set([]) # <<<<<<<<<<<<<< @@ -26925,7 +27241,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___warn_errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "cvcf.pyx":301 + /* "pysam/cvcf.pyx":301 * _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD * _warn_errors = set([]) * _leftalign = False # <<<<<<<<<<<<<< @@ -26937,7 +27253,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___leftalign, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":304 + /* "pysam/cvcf.pyx":304 * * # reference sequence * _reference = None # <<<<<<<<<<<<<< @@ -26946,7 +27262,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___reference, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":307 + /* "pysam/cvcf.pyx":307 * * # regions to include; None includes everything * _regions = None # <<<<<<<<<<<<<< @@ -26955,7 +27271,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___regions, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 307; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":310 + /* "pysam/cvcf.pyx":310 * * # statefull stuff * _lineno = -1 # <<<<<<<<<<<<<< @@ -26964,7 +27280,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___lineno, __pyx_int_neg_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":311 + /* "pysam/cvcf.pyx":311 * # statefull stuff * _lineno = -1 * _line = None # <<<<<<<<<<<<<< @@ -26973,7 +27289,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___line, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":312 + /* "pysam/cvcf.pyx":312 * _lineno = -1 * _line = None * _lines = None # <<<<<<<<<<<<<< @@ -26982,14 +27298,14 @@ PyMODINIT_FUNC PyInit_cvcf(void) */ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___lines, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "cvcf.pyx":314 + /* "pysam/cvcf.pyx":314 * _lines = None * * def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # <<<<<<<<<<<<<< * # make error identifiers accessible by name * for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_1__init__, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_174)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_1__init__, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_175)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -26997,31 +27313,31 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_CyFunction_Defaults(__pyx_defaults, __pyx_t_1)->__pyx_arg_leftalign = __pyx_t_3; __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_4cvcf_3VCF_85__defaults__); + __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_85__defaults__); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s____init__, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":335 + /* "pysam/cvcf.pyx":335 * self._lines = lines * * def error(self,line,error,opt=None): # <<<<<<<<<<<<<< * if error in self._ignored_errors: return * errorlabel, errorstring = self._errors[error].split(':') */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_3error, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_176)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_3error, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_177)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_177)); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_178)); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__error, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":344 + /* "pysam/cvcf.pyx":344 * raise ValueError(errorstring) * * def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<< * if self._version == 40: * if not format.startswith('<'): */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_5parse_format, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_179)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_5parse_format, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_180)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults1), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -27029,18 +27345,18 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_CyFunction_Defaults(__pyx_defaults1, __pyx_t_1)->__pyx_arg_filter = __pyx_t_3; __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_4cvcf_3VCF_87__defaults__); + __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_87__defaults__); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_format, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":416 + /* "pysam/cvcf.pyx":416 * return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) * * def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<< * values = [('ID',fmt.id)] * if fmt.number != None and not filter: */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_7format_format, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_181)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_7format_format, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_182)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults2), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -27048,42 +27364,42 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_CyFunction_Defaults(__pyx_defaults2, __pyx_t_1)->__pyx_arg_filter = __pyx_t_3; __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_4cvcf_3VCF_89__defaults__); + __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_89__defaults__); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__format_format, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":436 + /* "pysam/cvcf.pyx":436 * return format * * def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<< * fmt = formatdict[format] * if fmt.numbertype == self.NT_UNKNOWN: return -1 */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_9get_expected, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_183)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_9get_expected, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_184)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__get_expected, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":447 + /* "pysam/cvcf.pyx":447 * * * def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<< * if key in formatdict: return * self.error(line,self.ERROR_UNKNOWN_KEY,key) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_11_add_definition, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_185)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_11_add_definition, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_186)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___add_definition, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":464 + /* "pysam/cvcf.pyx":464 * * # todo: trim trailing missing values * def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<< * output, sdata = [], [] * if type(data) == type([]): # for FORMAT field, make data with dummy values */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_13format_formatdata, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_187)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_13format_formatdata, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_188)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults3), 2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -27096,126 +27412,126 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_t_1)->__pyx_arg_value = __pyx_t_3; __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_4cvcf_3VCF_91__defaults__); + __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_91__defaults__); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__format_formatdata, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":498 + /* "pysam/cvcf.pyx":498 * * * def enter_default_format(self): # <<<<<<<<<<<<<< * for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), * FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_15enter_default_format, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_189)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_15enter_default_format, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_190)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s_121, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":517 + /* "pysam/cvcf.pyx":517 * self._format[f.id] = f * * def parse_header( self, line ): # <<<<<<<<<<<<<< * assert line.startswith('##') * elts = line[2:].split('=') */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_17parse_header, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_191)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_17parse_header, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_192)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":546 + /* "pysam/cvcf.pyx":546 * * * def write_header( self, stream ): # <<<<<<<<<<<<<< * stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) * for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_19write_header, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_193)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_19write_header, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_194)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":553 + /* "pysam/cvcf.pyx":553 * * * def parse_heading( self, line ): # <<<<<<<<<<<<<< * assert line.startswith('#') * assert not line.startswith('##') */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_21parse_heading, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_195)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_21parse_heading, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_196)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_heading, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":581 + /* "pysam/cvcf.pyx":581 * self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) * * def write_heading( self, stream ): # <<<<<<<<<<<<<< * stream.write("#" + "\t".join(self._required + self._samples) + "\n") * */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_23write_heading, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_197)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_23write_heading, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_198)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_heading, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":584 + /* "pysam/cvcf.pyx":584 * stream.write("#" + "\t".join(self._required + self._samples) + "\n") * * def convertGT(self, GTstring): # <<<<<<<<<<<<<< * if GTstring == ".": return ["."] * try: */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_25convertGT, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_199)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_25convertGT, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_200)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__convertGT, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":596 + /* "pysam/cvcf.pyx":596 * return [".","|","."] * * def convertGTback(self, GTdata): # <<<<<<<<<<<<<< * return ''.join(map(str,GTdata)) * */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_27convertGTback, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_201)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_27convertGTback, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_202)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__convertGTback, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":599 + /* "pysam/cvcf.pyx":599 * return ''.join(map(str,GTdata)) * * def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<< * # To do: check that the right number of values is present * f = formatdict.get(key,None) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_29parse_formatdata, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_203)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_29parse_formatdata, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_204)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_formatdata, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":641 + /* "pysam/cvcf.pyx":641 * self.error(line,self.ERROR_INFO_STRING) * * def inregion(self, chrom, pos): # <<<<<<<<<<<<<< * if not self._regions: return True * for r in self._regions: */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_31inregion, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_205)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_31inregion, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_206)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__inregion, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":647 + /* "pysam/cvcf.pyx":647 * return False * * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< * cols = line.split('\t') * if len(cols) != len(self._samples)+9: */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_33parse_data, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_207)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_33parse_data, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_208)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults4), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -27223,312 +27539,312 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_CyFunction_Defaults(__pyx_defaults4, __pyx_t_1)->__pyx_arg_lineparse = __pyx_t_3; __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_4cvcf_3VCF_93__defaults__); + __Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_93__defaults__); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":857 + /* "pysam/cvcf.pyx":857 * * * def write_data(self, stream, data): # <<<<<<<<<<<<<< * required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples * for k in required: */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_35write_data, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_209)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_35write_data, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_210)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":886 + /* "pysam/cvcf.pyx":886 * stream.write( "\t".join(output) + "\n" ) * * def _parse_header(self, stream): # <<<<<<<<<<<<<< * self._lineno = 0 * for line in stream: */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_37_parse_header, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_211)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_37_parse_header, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_212)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___parse_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":899 + /* "pysam/cvcf.pyx":899 * return line * * def _parse(self, line, stream): # <<<<<<<<<<<<<< * # deal with files with header only * if line.startswith("##"): return */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_39_parse, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_213)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_39_parse, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_214)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___parse, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":917 + /* "pysam/cvcf.pyx":917 * ###################################################################################################### * * def getsamples(self): # <<<<<<<<<<<<<< * """ List of samples in VCF file """ * return self._samples */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_42getsamples, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_215)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_42getsamples, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_216)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getsamples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":921 + /* "pysam/cvcf.pyx":921 * return self._samples * * def setsamples(self,samples): # <<<<<<<<<<<<<< * """ List of samples in VCF file """ * self._samples = samples */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_44setsamples, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_217)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_44setsamples, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_218)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setsamples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":925 + /* "pysam/cvcf.pyx":925 * self._samples = samples * * def getheader(self): # <<<<<<<<<<<<<< * """ List of header key-value pairs (strings) """ * return self._header */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_46getheader, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_219)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_46getheader, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_220)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":929 + /* "pysam/cvcf.pyx":929 * return self._header * * def setheader(self,header): # <<<<<<<<<<<<<< * """ List of header key-value pairs (strings) """ * self._header = header */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_48setheader, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_221)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_48setheader, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_222)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":933 + /* "pysam/cvcf.pyx":933 * self._header = header * * def getinfo(self): # <<<<<<<<<<<<<< * """ Dictionary of ##INFO tags, as VCF.FORMAT values """ * return self._info */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_50getinfo, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_223)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_50getinfo, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_224)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getinfo, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":937 + /* "pysam/cvcf.pyx":937 * return self._info * * def setinfo(self,info): # <<<<<<<<<<<<<< * """ Dictionary of ##INFO tags, as VCF.FORMAT values """ * self._info = info */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_52setinfo, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_225)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_52setinfo, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_226)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setinfo, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":941 + /* "pysam/cvcf.pyx":941 * self._info = info * * def getformat(self): # <<<<<<<<<<<<<< * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * return self._format */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_54getformat, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_227)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_54getformat, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_228)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getformat, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":945 + /* "pysam/cvcf.pyx":945 * return self._format * * def setformat(self,format): # <<<<<<<<<<<<<< * """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ * self._format = format */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_56setformat, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_229)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_56setformat, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_230)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setformat, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":949 + /* "pysam/cvcf.pyx":949 * self._format = format * * def getfilter(self): # <<<<<<<<<<<<<< * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * return self._filter */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_58getfilter, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_231)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_58getfilter, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_232)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getfilter, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":953 + /* "pysam/cvcf.pyx":953 * return self._filter * * def setfilter(self,filter): # <<<<<<<<<<<<<< * """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ * self._filter = filter */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_60setfilter, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_233)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_60setfilter, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_234)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setfilter, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":957 + /* "pysam/cvcf.pyx":957 * self._filter = filter * * def setversion(self, version): # <<<<<<<<<<<<<< * if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") * self._version = version */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_62setversion, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_235)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_62setversion, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_236)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setversion, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":961 + /* "pysam/cvcf.pyx":961 * self._version = version * * def setregions(self, regions): # <<<<<<<<<<<<<< * self._regions = regions * */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_64setregions, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_237)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_64setregions, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_238)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setregions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":964 + /* "pysam/cvcf.pyx":964 * self._regions = regions * * def setreference(self, ref): # <<<<<<<<<<<<<< * """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """ * self._reference = ref */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_66setreference, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_239)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_66setreference, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_240)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setreference, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":968 + /* "pysam/cvcf.pyx":968 * self._reference = ref * * def ignoreerror(self, errorstring): # <<<<<<<<<<<<<< * try: self._ignored_errors.add(self.__dict__[errorstring]) * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_68ignoreerror, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_241)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_68ignoreerror, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_242)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__ignoreerror, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":972 + /* "pysam/cvcf.pyx":972 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) * * def warnerror(self, errorstring): # <<<<<<<<<<<<<< * try: self._warn_errors.add(self.__dict__[errorstring]) * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_70warnerror, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_243)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_70warnerror, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_244)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__warnerror, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":976 + /* "pysam/cvcf.pyx":976 * except KeyError: raise ValueError("Invalid error string: %s" % errorstring) * * def parse(self, stream): # <<<<<<<<<<<<<< * """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ * last_line = self._parse_header(stream) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_72parse, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_245)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_72parse, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_246)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":983 + /* "pysam/cvcf.pyx":983 * return self._parse(last_line, stream) * * def write(self, stream, datagenerator): # <<<<<<<<<<<<<< * """ Writes a VCF file to a stream, using a data generator (or list) """ * self.write_header(stream) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_74write, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_247)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_74write, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_248)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":989 + /* "pysam/cvcf.pyx":989 * for data in datagenerator: self.write_data(stream,data) * * def writeheader(self, stream): # <<<<<<<<<<<<<< * """ Writes a VCF header """ * self.write_header(stream) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_76writeheader, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_249)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_76writeheader, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_250)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__writeheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":994 + /* "pysam/cvcf.pyx":994 * self.write_heading(stream) * * def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<< * """ Utility function: compares two calls for equality """ * # a variant should always be assigned to a unique position, one base before */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_78compare_calls, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_251)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_78compare_calls, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_252)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__compare_calls, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":1016 + /* "pysam/cvcf.pyx":1016 * ########################################################################################################### * * def connect( self, filename ): # <<<<<<<<<<<<<< * '''connect to tabix file.''' * self.tabixfile = pysam.Tabixfile( filename ) */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_80connect, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_253)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_80connect, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_254)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__connect, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":1021 + /* "pysam/cvcf.pyx":1021 * self._parse_header(self.tabixfile.header) * * def fetch(self, # <<<<<<<<<<<<<< * reference = None, * start = None, */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_82fetch, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_255)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_82fetch, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_256)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_256)); + __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_257)); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__fetch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":1030 + /* "pysam/cvcf.pyx":1030 * return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) ) * * def validate( self, record ): # <<<<<<<<<<<<<< * '''validate vcf record. * */ - __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_84validate, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_258)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_84validate, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_259)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__validate, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "cvcf.pyx":237 + /* "pysam/cvcf.pyx":237 * return r * * class VCF(object): # <<<<<<<<<<<<<< @@ -27540,14 +27856,14 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_INCREF(__pyx_builtin_object); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_builtin_object); __Pyx_GIVEREF(__pyx_builtin_object); - __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s__cvcf); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s_135); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VCF, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - /* "cvcf.pyx":1155 + /* "pysam/cvcf.pyx":1155 * pos -= 1 * * __all__ = [ # <<<<<<<<<<<<<< @@ -27565,7 +27881,7 @@ PyMODINIT_FUNC PyInit_cvcf(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - /* "cvcf.pyx":1 + /* "pysam/cvcf.pyx":1 * # # <<<<<<<<<<<<<< * # Code to read, write and edit VCF files * # @@ -27580,10 +27896,10 @@ PyMODINIT_FUNC PyInit_cvcf(void) __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); if (__pyx_m) { - __Pyx_AddTraceback("init cvcf", __pyx_clineno, __pyx_lineno, __pyx_filename); + __Pyx_AddTraceback("init pysam.cvcf", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { - PyErr_SetString(PyExc_ImportError, "init cvcf"); + PyErr_SetString(PyExc_ImportError, "init pysam.cvcf"); } __pyx_L0:; __Pyx_RefNannyFinishContext(); @@ -27646,7 +27962,7 @@ static void __Pyx_RaiseArgtupleInvalid( more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, - "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)", + "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } @@ -27660,7 +27976,7 @@ static void __Pyx_RaiseDoubleKeywordsError( "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, - PyString_AS_STRING(kw_name)); + PyString_AsString(kw_name)); #endif } @@ -27681,48 +27997,72 @@ static int __Pyx_ParseOptionalKeywords( while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; - } else { - #if PY_MAJOR_VERSION < 3 - if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { - #else - if (unlikely(!PyUnicode_Check(key))) { - #endif - goto invalid_keyword_type; - } else { - for (name = first_kw_arg; *name; name++) { - #if PY_MAJOR_VERSION >= 3 - if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && - PyUnicode_Compare(**name, key) == 0) break; - #else - if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && - _PyString_Eq(**name, key)) break; - #endif - } - if (*name) { + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { values[name-argnames] = value; - } else { - for (name=argnames; name != first_kw_arg; name++) { - if (**name == key) goto arg_passed_twice; - #if PY_MAJOR_VERSION >= 3 - if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) && - PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice; - #else - if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) && - _PyString_Eq(**name, key)) goto arg_passed_twice; - #endif - } - if (kwds2) { - if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; - } else { - goto invalid_keyword; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; } } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; } } return 0; arg_passed_twice: - __Pyx_RaiseDoubleKeywordsError(function_name, **name); + __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, @@ -27741,10 +28081,9 @@ bad: return -1; } - - static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; @@ -27753,19 +28092,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif - *type = local_type; - *value = local_value; - *tb = local_tb; Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; @@ -27773,10 +28120,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF - these objects (XDECREF may run arbitrary code). */ + these objects (DECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif return 0; bad: *type = 0; @@ -27823,33 +28173,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); - Py_XINCREF(value); - Py_XINCREF(tb); - if (tb == Py_None) { - Py_DECREF(tb); - tb = 0; - } - else if (tb != NULL && !PyTraceBack_Check(tb)) { - PyErr_SetString(PyExc_TypeError, - "raise: arg 3 must be a traceback or None"); - goto raise_error; - } - if (value == NULL) { - value = Py_None; + if (!value || value == Py_None) + value = NULL; + else Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } } #if PY_VERSION_HEX < 0x02050000 - if (!PyClass_Check(type)) + if (PyClass_Check(type)) { #else - if (!PyType_Check(type)) + if (PyType_Check(type)) { #endif - { - if (value != Py_None) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } - Py_DECREF(value); value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { @@ -27882,6 +28237,7 @@ raise_error: } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { @@ -27899,12 +28255,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } value = type; type = (PyObject*) Py_TYPE(value); - } else if (!PyExceptionClass_Check(type)) { + } else if (PyExceptionClass_Check(type)) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } + else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyEval_CallObject(type, args); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } - if (cause) { + if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); @@ -27921,9 +28301,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject "BaseException"); goto bad; } - if (!value) { - value = PyObject_CallObject(type, NULL); - } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); @@ -27937,12 +28314,16 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } } bad: + Py_XDECREF(owned_instance); return; } #endif static double __Pyx__PyObject_AsDouble(PyObject* obj) { PyObject* float_value; +#if CYTHON_COMPILING_IN_PYPY + float_value = PyNumber_Float(obj); +#else if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) { return PyFloat_AsDouble(obj); } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) { @@ -27959,6 +28340,7 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj) { PyTuple_SET_ITEM(args, 0, 0); Py_DECREF(args); } +#endif if (likely(float_value)) { double value = PyFloat_AS_DOUBLE(float_value); Py_DECREF(float_value); @@ -27972,19 +28354,49 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } -static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { - PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable"); +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, - "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack", + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } -static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { - PyErr_Format(PyExc_ValueError, - "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected); +static CYTHON_INLINE int __Pyx_IterFinish(void) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + PyObject* exc_type = tstate->curexc_type; + if (unlikely(exc_type)) { + if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { + PyObject *exc_value, *exc_tb; + exc_value = tstate->curexc_value; + exc_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; + Py_DECREF(exc_type); + Py_XDECREF(exc_value); + Py_XDECREF(exc_tb); + return 0; + } else { + return -1; + } + } + return 0; +#else + if (unlikely(PyErr_Occurred())) { + if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { + PyErr_Clear(); + return 0; + } else { + return -1; + } + } + return 0; +#endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { @@ -27992,13 +28404,8 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; - } else if (PyErr_Occurred()) { - if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { - PyErr_Clear(); - return 0; - } else { - return -1; - } + } else { + return __Pyx_IterFinish(); } return 0; } @@ -28010,13 +28417,197 @@ static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) return q; } +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { + if (t == Py_None) { + __Pyx_RaiseNoneNotIterableError(); + } else if (PyTuple_GET_SIZE(t) < index) { + __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); + } else { + __Pyx_RaiseTooManyValuesError(index); + } +} + +static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, + int is_tuple, int has_known_size, int decref_tuple) { + Py_ssize_t index; + PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; + if (!is_tuple && unlikely(!PyTuple_Check(tuple))) { + iternextfunc iternext; + iter = PyObject_GetIter(tuple); + if (unlikely(!iter)) goto bad; + if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; } + iternext = Py_TYPE(iter)->tp_iternext; + value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; } + value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; } + if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad; + Py_DECREF(iter); + } else { + if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) { + __Pyx_UnpackTupleError(tuple, 2); + goto bad; + } +#if CYTHON_COMPILING_IN_PYPY + value1 = PySequence_ITEM(tuple, 0); + if (unlikely(!value1)) goto bad; + value2 = PySequence_ITEM(tuple, 1); + if (unlikely(!value2)) goto bad; +#else + value1 = PyTuple_GET_ITEM(tuple, 0); + value2 = PyTuple_GET_ITEM(tuple, 1); + Py_INCREF(value1); + Py_INCREF(value2); +#endif + if (decref_tuple) { Py_DECREF(tuple); } + } + *pvalue1 = value1; + *pvalue2 = value2; + return 0; +unpacking_failed: + if (!has_known_size && __Pyx_IterFinish() == 0) + __Pyx_RaiseNeedMoreValuesError(index); +bad: + Py_XDECREF(iter); + Py_XDECREF(value1); + Py_XDECREF(value2); + if (decref_tuple) { Py_XDECREF(tuple); } + return -1; +} +static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, + Py_ssize_t* p_orig_length, int* p_source_is_dict) { + is_dict = is_dict || likely(PyDict_CheckExact(iterable)); + *p_source_is_dict = is_dict; +#if !CYTHON_COMPILING_IN_PYPY + if (is_dict) { + *p_orig_length = PyDict_Size(iterable); + Py_INCREF(iterable); + return iterable; + } +#endif + *p_orig_length = 0; + if (method_name) { + PyObject* iter; + iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL); + if (!iterable) + return NULL; +#if !CYTHON_COMPILING_IN_PYPY + if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable)) + return iterable; +#endif + iter = PyObject_GetIter(iterable); + Py_DECREF(iterable); + return iter; + } + return PyObject_GetIter(iterable); +} +static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos, + PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) { + PyObject* next_item; +#if !CYTHON_COMPILING_IN_PYPY + if (source_is_dict) { + PyObject *key, *value; + if (unlikely(orig_length != PyDict_Size(iter_obj))) { + PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration"); + return -1; + } + if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) { + return 0; + } + if (pitem) { + PyObject* tuple = PyTuple_New(2); + if (unlikely(!tuple)) { + return -1; + } + Py_INCREF(key); + Py_INCREF(value); + PyTuple_SET_ITEM(tuple, 0, key); + PyTuple_SET_ITEM(tuple, 1, value); + *pitem = tuple; + } else { + if (pkey) { + Py_INCREF(key); + *pkey = key; + } + if (pvalue) { + Py_INCREF(value); + *pvalue = value; + } + } + return 1; + } else if (PyTuple_CheckExact(iter_obj)) { + Py_ssize_t pos = *ppos; + if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0; + *ppos = pos + 1; + next_item = PyTuple_GET_ITEM(iter_obj, pos); + Py_INCREF(next_item); + } else if (PyList_CheckExact(iter_obj)) { + Py_ssize_t pos = *ppos; + if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0; + *ppos = pos + 1; + next_item = PyList_GET_ITEM(iter_obj, pos); + Py_INCREF(next_item); + } else +#endif + { + next_item = PyIter_Next(iter_obj); + if (unlikely(!next_item)) { + return __Pyx_IterFinish(); + } + } + if (pitem) { + *pitem = next_item; + } else if (pkey && pvalue) { + if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1)) + return -1; + } else if (pkey) { + *pkey = next_item; + } else { + *pvalue = next_item; + } + return 1; +} static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); } +static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) { + PyTypeObject* type = Py_TYPE(obj); + while (type && type->tp_dealloc != current_tp_dealloc) + type = type->tp_base; + while (type && type->tp_dealloc == current_tp_dealloc) + type = type->tp_base; + if (type) + type->tp_dealloc(obj); +} + +static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { + PyTypeObject* type = Py_TYPE(obj); + while (type && type->tp_traverse != current_tp_traverse) + type = type->tp_base; + while (type && type->tp_traverse == current_tp_traverse) + type = type->tp_base; + if (type && type->tp_traverse) + return type->tp_traverse(obj, v, a); + return 0; +} + +static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { + PyTypeObject* type = Py_TYPE(obj); + while (type && type->tp_clear != current_tp_clear) + type = type->tp_base; + while (type && type->tp_clear == current_tp_clear) + type = type->tp_base; + if (type && type->tp_clear) + type->tp_clear(obj); +} + static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; @@ -28024,8 +28615,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; @@ -28037,6 +28632,9 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(type, value, tb); +#endif } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { @@ -28119,7 +28717,6 @@ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) { static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { PyObject *metaclass; - /* Default metaclass */ #if PY_MAJOR_VERSION < 3 if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); @@ -28149,7 +28746,6 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na PyObject *metaclass; if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; - /* Python2 __metaclass__ */ metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { Py_INCREF(metaclass); @@ -28441,6 +29037,56 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) PyString_AsString(func_name), (void *)op); #endif } +#if CYTHON_COMPILING_IN_PYPY +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyCFunctionObject* f = (PyCFunctionObject*)func; + PyCFunction meth = PyCFunction_GET_FUNCTION(func); + PyObject *self = PyCFunction_GET_SELF(func); + Py_ssize_t size; + switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) { + case METH_VARARGS: + if (likely(kw == NULL) || PyDict_Size(kw) == 0) + return (*meth)(self, arg); + break; + case METH_VARARGS | METH_KEYWORDS: + return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); + case METH_NOARGS: + if (likely(kw == NULL) || PyDict_Size(kw) == 0) { + size = PyTuple_GET_SIZE(arg); + if (size == 0) + return (*meth)(self, NULL); + PyErr_Format(PyExc_TypeError, + "%.200s() takes no arguments (%zd given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + case METH_O: + if (likely(kw == NULL) || PyDict_Size(kw) == 0) { + size = PyTuple_GET_SIZE(arg); + if (size == 1) + return (*meth)(self, PyTuple_GET_ITEM(arg, 0)); + PyErr_Format(PyExc_TypeError, + "%.200s() takes exactly one argument (%zd given)", + f->m_ml->ml_name, size); + return NULL; + } + break; + default: + PyErr_SetString(PyExc_SystemError, "Bad call flags in " + "__Pyx_CyFunction_Call. METH_OLDARGS is no " + "longer supported!"); + return NULL; + } + PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", + f->m_ml->ml_name); + return NULL; +} +#else +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + return PyCFunction_Call(func, arg, kw); +} +#endif static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ @@ -28460,7 +29106,7 @@ static PyTypeObject __pyx_CyFunctionType_type = { 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ - __Pyx_PyCFunction_Call, /*tp_call*/ + __Pyx_CyFunction_Call, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ @@ -28496,15 +29142,16 @@ static PyTypeObject __pyx_CyFunctionType_type = { 0, /*tp_version_tag*/ #endif }; -static int __Pyx_CyFunction_init(void) -{ +static int __Pyx_CyFunction_init(void) { +#if !CYTHON_COMPILING_IN_PYPY + __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; +#endif if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; } -void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) -{ +static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults = PyMem_Malloc(size); if (!m->defaults) @@ -28513,8 +29160,7 @@ void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) m->defaults_pyobjects = pyobjects; return m->defaults; } -static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) -{ +static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults_tuple = tuple; Py_INCREF(tuple); @@ -28545,78 +29191,6 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { } } -static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { - if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) { - return (equals == Py_NE); - } else if (PyBytes_GET_SIZE(s1) == 1) { - if (equals == Py_EQ) - return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]); - else - return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]); - } else { - int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1)); - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -} - -static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { - if (s1 == s2) { - return (equals == Py_EQ); - } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { - #if CYTHON_PEP393_ENABLED - if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0)) - return -1; - if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) { - return (equals == Py_NE); - } else if (PyUnicode_GET_LENGTH(s1) == 1) { - Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0); - Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0); - return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); - #else - if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { - return (equals == Py_NE); - } else if (PyUnicode_GET_SIZE(s1) == 1) { - Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0]; - Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0]; - return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); - #endif - } else { - int result = PyUnicode_Compare(s1, s2); - if ((result == -1) && unlikely(PyErr_Occurred())) - return -1; - return (equals == Py_EQ) ? (result == 0) : (result != 0); - } - } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) { - return (equals == Py_NE); - } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) { - return (equals == Py_NE); - } else { - int result; - PyObject* py_result = PyObject_RichCompare(s1, s2, equals); - if (!py_result) - return -1; - result = __Pyx_PyObject_IsTrue(py_result); - Py_DECREF(py_result); - return result; - } -} - static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; @@ -29019,6 +29593,7 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; +#if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; @@ -29026,6 +29601,10 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, tstate->exc_type = *type; tstate->exc_value = *value; tstate->exc_traceback = *tb; +#else + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); +#endif *type = tmp_type; *value = tmp_value; *tb = tmp_tb; @@ -29035,9 +29614,70 @@ static PyObject *__Pyx_Generator_Next(PyObject *self); static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); static PyObject *__Pyx_Generator_Close(PyObject *self); static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args); +static PyTypeObject *__pyx_GeneratorType = 0; +#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType) +#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom) +#if 1 || PY_VERSION_HEX < 0x030300B0 +static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) { + PyObject *et, *ev, *tb; + PyObject *value = NULL; + __Pyx_ErrFetch(&et, &ev, &tb); + if (!et) { + Py_XDECREF(tb); + Py_XDECREF(ev); + Py_INCREF(Py_None); + *pvalue = Py_None; + return 0; + } + if (unlikely(et != PyExc_StopIteration) && + unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) { + __Pyx_ErrRestore(et, ev, tb); + return -1; + } + if (likely(et == PyExc_StopIteration)) { + if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) { + if (!ev) { + Py_INCREF(Py_None); + ev = Py_None; + } + Py_XDECREF(tb); + Py_DECREF(et); + *pvalue = ev; + return 0; + } + } + PyErr_NormalizeException(&et, &ev, &tb); + if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) { + __Pyx_ErrRestore(et, ev, tb); + return -1; + } + Py_XDECREF(tb); + Py_DECREF(et); +#if PY_VERSION_HEX >= 0x030300A0 + value = ((PyStopIterationObject *)ev)->value; + Py_INCREF(value); + Py_DECREF(ev); +#else + { + PyObject* args = PyObject_GetAttrString(ev, "args"); + Py_DECREF(ev); + if (likely(args)) { + value = PyObject_GetItem(args, 0); + Py_DECREF(args); + } + if (unlikely(!value)) { + __Pyx_ErrRestore(NULL, NULL, NULL); + Py_INCREF(Py_None); + value = Py_None; + } + } +#endif + *pvalue = value; + return 0; +} +#endif static CYTHON_INLINE -void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) -{ +void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) { PyObject *exc_type = self->exc_type; PyObject *exc_value = self->exc_value; PyObject *exc_traceback = self->exc_traceback; @@ -29049,14 +29689,18 @@ void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) Py_XDECREF(exc_traceback); } static CYTHON_INLINE -PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) -{ - PyObject *retval; - if (unlikely(self->is_running)) { +int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) { + if (unlikely(gen->is_running)) { PyErr_SetString(PyExc_ValueError, "generator already executing"); - return NULL; + return 1; } + return 0; +} +static CYTHON_INLINE +PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) { + PyObject *retval; + assert(!self->is_running); if (unlikely(self->resume_label == 0)) { if (unlikely(value && value != Py_None)) { PyErr_SetString(PyExc_TypeError, @@ -29069,81 +29713,240 @@ PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) PyErr_SetNone(PyExc_StopIteration); return NULL; } - if (value) - __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); - else + if (value) { +#if CYTHON_COMPILING_IN_PYPY +#else + /* Generators always return to their most recent caller, not + * necessarily their creator. */ + if (self->exc_traceback) { + PyThreadState *tstate = PyThreadState_GET(); + PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; + PyFrameObject *f = tb->tb_frame; + Py_XINCREF(tstate->frame); + assert(f->f_back == NULL); + f->f_back = tstate->frame; + } +#endif + __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, + &self->exc_traceback); + } else { __Pyx_Generator_ExceptionClear(self); + } self->is_running = 1; retval = self->body((PyObject *) self, value); self->is_running = 0; - if (retval) - __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); - else + if (retval) { + __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, + &self->exc_traceback); +#if CYTHON_COMPILING_IN_PYPY +#else + /* Don't keep the reference to f_back any longer than necessary. It + * may keep a chain of frames alive or it could create a reference + * cycle. */ + if (self->exc_traceback) { + PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; + PyFrameObject *f = tb->tb_frame; + Py_CLEAR(f->f_back); + } +#endif + } else { __Pyx_Generator_ExceptionClear(self); + } return retval; } -static PyObject *__Pyx_Generator_Next(PyObject *self) -{ - return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None); +static CYTHON_INLINE +PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) { + PyObject *ret; + PyObject *val = NULL; + __Pyx_Generator_Undelegate(gen); + __Pyx_PyGen_FetchStopIterationValue(&val); + ret = __Pyx_Generator_SendEx(gen, val); + Py_XDECREF(val); + return ret; +} +static PyObject *__Pyx_Generator_Next(PyObject *self) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; + PyObject *yf = gen->yieldfrom; + if (unlikely(__Pyx_Generator_CheckRunning(gen))) + return NULL; + if (yf) { + PyObject *ret; + gen->is_running = 1; + ret = Py_TYPE(yf)->tp_iternext(yf); + gen->is_running = 0; + if (likely(ret)) { + return ret; + } + return __Pyx_Generator_FinishDelegation(gen); + } + return __Pyx_Generator_SendEx(gen, Py_None); } -static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) -{ - return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value); +static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; + PyObject *yf = gen->yieldfrom; + if (unlikely(__Pyx_Generator_CheckRunning(gen))) + return NULL; + if (yf) { + PyObject *ret; + gen->is_running = 1; + if (__Pyx_Generator_CheckExact(yf)) { + ret = __Pyx_Generator_Send(yf, value); + } else { + if (value == Py_None) + ret = PyIter_Next(yf); + else + ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value); + } + gen->is_running = 0; + if (likely(ret)) { + return ret; + } + return __Pyx_Generator_FinishDelegation(gen); + } + return __Pyx_Generator_SendEx(gen, value); } -static PyObject *__Pyx_Generator_Close(PyObject *self) -{ - __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; - PyObject *retval; +static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) { + PyObject *retval = NULL; + int err = 0; + if (__Pyx_Generator_CheckExact(yf)) { + retval = __Pyx_Generator_Close(yf); + if (!retval) + return -1; + } else { + PyObject *meth; + gen->is_running = 1; + meth = PyObject_GetAttrString(yf, "close"); + if (unlikely(!meth)) { + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { + PyErr_WriteUnraisable(yf); + } + PyErr_Clear(); + } else { + retval = PyObject_CallFunction(meth, NULL); + Py_DECREF(meth); + if (!retval) + err = -1; + } + gen->is_running = 0; + } + Py_XDECREF(retval); + return err; +} +static PyObject *__Pyx_Generator_Close(PyObject *self) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; + PyObject *retval, *raised_exception; + PyObject *yf = gen->yieldfrom; + int err = 0; + if (unlikely(__Pyx_Generator_CheckRunning(gen))) + return NULL; + if (yf) { + Py_INCREF(yf); + err = __Pyx_Generator_CloseIter(gen, yf); + __Pyx_Generator_Undelegate(gen); + Py_DECREF(yf); + } + if (err == 0) #if PY_VERSION_HEX < 0x02050000 - PyErr_SetNone(PyExc_StopIteration); + PyErr_SetNone(PyExc_StopIteration); #else - PyErr_SetNone(PyExc_GeneratorExit); + PyErr_SetNone(PyExc_GeneratorExit); #endif - retval = __Pyx_Generator_SendEx(generator, NULL); + retval = __Pyx_Generator_SendEx(gen, NULL); if (retval) { Py_DECREF(retval); PyErr_SetString(PyExc_RuntimeError, "generator ignored GeneratorExit"); return NULL; } -#if PY_VERSION_HEX < 0x02050000 - if (PyErr_ExceptionMatches(PyExc_StopIteration)) -#else - if (PyErr_ExceptionMatches(PyExc_StopIteration) - || PyErr_ExceptionMatches(PyExc_GeneratorExit)) + raised_exception = PyErr_Occurred(); + if (!raised_exception + || raised_exception == PyExc_StopIteration +#if PY_VERSION_HEX >= 0x02050000 + || raised_exception == PyExc_GeneratorExit + || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit) #endif + || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration)) { - PyErr_Clear(); /* ignore these errors */ + if (raised_exception) PyErr_Clear(); /* ignore these errors */ Py_INCREF(Py_None); return Py_None; } return NULL; } -static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) -{ - __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; +static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject *typ; PyObject *tb = NULL; PyObject *val = NULL; + PyObject *yf = gen->yieldfrom; if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) return NULL; + if (unlikely(__Pyx_Generator_CheckRunning(gen))) + return NULL; + if (yf) { + PyObject *ret; + Py_INCREF(yf); +#if PY_VERSION_HEX >= 0x02050000 + if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) { + int err = __Pyx_Generator_CloseIter(gen, yf); + Py_DECREF(yf); + __Pyx_Generator_Undelegate(gen); + if (err < 0) + return __Pyx_Generator_SendEx(gen, NULL); + goto throw_here; + } +#endif + gen->is_running = 1; + if (__Pyx_Generator_CheckExact(yf)) { + ret = __Pyx_Generator_Throw(yf, args); + } else { + PyObject *meth = PyObject_GetAttrString(yf, "throw"); + if (unlikely(!meth)) { + Py_DECREF(yf); + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { + gen->is_running = 0; + return NULL; + } + PyErr_Clear(); + __Pyx_Generator_Undelegate(gen); + gen->is_running = 0; + goto throw_here; + } + ret = PyObject_CallObject(meth, args); + Py_DECREF(meth); + } + gen->is_running = 0; + Py_DECREF(yf); + if (!ret) { + ret = __Pyx_Generator_FinishDelegation(gen); + } + return ret; + } +throw_here: __Pyx_Raise(typ, val, tb, NULL); - return __Pyx_Generator_SendEx(generator, NULL); + return __Pyx_Generator_SendEx(gen, NULL); } -static int -__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) -{ +static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_VISIT(gen->closure); Py_VISIT(gen->classobj); + Py_VISIT(gen->yieldfrom); Py_VISIT(gen->exc_type); Py_VISIT(gen->exc_value); Py_VISIT(gen->exc_traceback); return 0; } -static void -__Pyx_Generator_dealloc(PyObject *self) -{ +static int __Pyx_Generator_clear(PyObject *self) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; + Py_CLEAR(gen->closure); + Py_CLEAR(gen->classobj); + Py_CLEAR(gen->yieldfrom); + Py_CLEAR(gen->exc_type); + Py_CLEAR(gen->exc_value); + Py_CLEAR(gen->exc_traceback); + return 0; +} +static void __Pyx_Generator_dealloc(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject_GC_UnTrack(gen); if (gen->gi_weakreflist != NULL) @@ -29155,16 +29958,10 @@ __Pyx_Generator_dealloc(PyObject *self) return; /* resurrected. :( */ } PyObject_GC_UnTrack(self); - Py_CLEAR(gen->closure); - Py_CLEAR(gen->classobj); - Py_CLEAR(gen->exc_type); - Py_CLEAR(gen->exc_value); - Py_CLEAR(gen->exc_traceback); + __Pyx_Generator_clear(self); PyObject_GC_Del(gen); } -static void -__Pyx_Generator_del(PyObject *self) -{ +static void __Pyx_Generator_del(PyObject *self) { PyObject *res; PyObject *error_type, *error_value, *error_traceback; __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; @@ -29193,11 +29990,13 @@ __Pyx_Generator_del(PyObject *self) _Py_NewReference(self); self->ob_refcnt = refcnt; } +#if CYTHON_COMPILING_FOR_CPYTHON assert(PyType_IS_GC(self->ob_type) && _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so * we need to undo that. */ _Py_DEC_REFTOTAL; +#endif /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object * chain, so no more to do there. * If COUNT_ALLOCS, the original decref bumped tp_frees, and @@ -29205,13 +30004,17 @@ __Pyx_Generator_del(PyObject *self) * undone. */ #ifdef COUNT_ALLOCS - --self->ob_type->tp_frees; - --self->ob_type->tp_allocs; + --Py_TYPE(self)->tp_frees; + --Py_TYPE(self)->tp_allocs; #endif } static PyMemberDef __pyx_Generator_memberlist[] = { {(char *) "gi_running", - T_INT, +#if PY_VERSION_HEX >= 0x02060000 + T_BOOL, +#else + T_BYTE, +#endif offsetof(__pyx_GeneratorObject, is_running), READONLY, NULL}, @@ -29223,7 +30026,7 @@ static PyMethodDef __pyx_Generator_methods[] = { {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0}, {0, 0, 0, 0} }; -static PyTypeObject __pyx_GeneratorType = { +static PyTypeObject __pyx_GeneratorType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("generator"), /*tp_name*/ sizeof(__pyx_GeneratorObject), /*tp_basicsize*/ @@ -29244,7 +30047,7 @@ static PyTypeObject __pyx_GeneratorType = { 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ - PyObject_GenericGetAttr, /*tp_getattro*/ + 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ @@ -29253,7 +30056,7 @@ static PyTypeObject __pyx_GeneratorType = { 0, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */ - PyObject_SelfIter, /*tp_iter*/ + 0, /*tp_iter*/ (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/ __pyx_Generator_methods, /*tp_methods*/ __pyx_Generator_memberlist, /*tp_members*/ @@ -29278,12 +30081,10 @@ static PyTypeObject __pyx_GeneratorType = { 0, /*tp_version_tag*/ #endif }; -static -__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, - PyObject *closure) -{ +static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, + PyObject *closure) { __pyx_GeneratorObject *gen = - PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType); + PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type); if (gen == NULL) return NULL; gen->body = body; @@ -29292,6 +30093,7 @@ __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, gen->is_running = 0; gen->resume_label = 0; gen->classobj = NULL; + gen->yieldfrom = NULL; gen->exc_type = NULL; gen->exc_value = NULL; gen->exc_traceback = NULL; @@ -29299,9 +30101,14 @@ __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject_GC_Track(gen); return gen; } -static int __pyx_Generator_init(void) -{ - return PyType_Ready(&__pyx_GeneratorType); +static int __pyx_Generator_init(void) { + __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr; + __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter; + if (PyType_Ready(&__pyx_GeneratorType_type)) { + return -1; + } + __pyx_GeneratorType = &__pyx_GeneratorType_type; + return 0; } static int __Pyx_check_binary_version(void) { @@ -29323,6 +30130,23 @@ static int __Pyx_check_binary_version(void) { return 0; } +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, @@ -29375,23 +30199,6 @@ bad: } #endif -#ifndef __PYX_HAVE_RT_ImportModule -#define __PYX_HAVE_RT_ImportModule -static PyObject *__Pyx_ImportModule(const char *name) { - PyObject *py_name = 0; - PyObject *py_module = 0; - py_name = __Pyx_PyIdentifier_FromString(name); - if (!py_name) - goto bad; - py_module = PyImport_Import(py_name); - Py_DECREF(py_name); - return py_module; -bad: - Py_XDECREF(py_name); - return 0; -} -#endif - static void* __Pyx_GetVtable(PyObject *dict) { void* ptr; PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__"); diff --git a/pysam/cvcf.pyx b/pysam/cvcf.pyx index 86ff882..edde706 100644 --- a/pysam/cvcf.pyx +++ b/pysam/cvcf.pyx @@ -47,8 +47,8 @@ from collections import namedtuple, defaultdict from operator import itemgetter import sys, re, copy, bisect -cimport ctabix -cimport TabProxies +from pysam cimport ctabix +from pysam cimport TabProxies import pysam gtsRegEx = re.compile("[|/\\\\]") diff --git a/pysam/version.py b/pysam/version.py index 48345d8..eb98027 100644 --- a/pysam/version.py +++ b/pysam/version.py @@ -1,6 +1,6 @@ # pysam versioning information -__version__ = "0.7.2" +__version__ = "0.7.3" __samtools_version__ = "0.1.18" diff --git a/setup.py b/setup.py index 7dfc9e0..182c30f 100644 --- a/setup.py +++ b/setup.py @@ -4,8 +4,6 @@ pysam ***** -For more information, see http://code.google.com/p/pysam. - ''' import os, sys, glob, shutil, hashlib, re, fnmatch @@ -116,10 +114,19 @@ if len(sys.argv) >= 2 and sys.argv[1] == "refresh": sys.exit(0) + +################### +# populate headers +# mkdir pysam/include pysam/include/win32 +# touch pysam/include/__init__.py pysam/include/win32/__init__.py +# cp samtools/*.h pysam/*.h pysam/include +# cp samtools/win32/*.h pysam/include/win32 + + from distribute_setup import use_setuptools use_setuptools() -from setuptools import Extension, setup +from setuptools import Extension, setup, find_packages ####################################################### ####################################################### @@ -129,8 +136,8 @@ except ImportError: # no Cython available - use existing C code cmdclass = { } csamtools_sources = [ "pysam/csamtools.c" ] - tabix_sources = [ "pysam/tabix.c" ] - tabproxies_sources = ["pysam/TabProxies.c" ] + tabix_sources = [ "pysam/ctabix.c" ] + tabproxies_sourcess = ["pysam/TabProxies.c" ] cvcf_sources = ["pysam/cvcf.c" ] else: cmdclass = { 'build_ext' : build_ext } @@ -221,27 +228,16 @@ metadata = { 'license': "MIT", 'platforms': "ALL", 'url': "http://code.google.com/p/pysam/", - 'py_modules': [ - "pysam/__init__", - "pysam/Pileup", - "pysam/version" ], - # cython larger that 0.16 for yield support - 'requires' : ['cython (>=0.16)'], + 'packages' : find_packages(), + 'requires' : ['cython (>=0.17)'], 'ext_modules': [samtools, tabix, tabproxies, cvcf ], 'cmdclass' : cmdclass, - 'install_requires' : ['cython>=0.16',], - 'data_files' : [('pysam', glob.glob('pysam/*.pxd')), - ('include/pysam', glob.glob('pysam/*.h')), - ('include/samtools', glob.glob('samtools/*.h')), - ('include/samtools/win32', glob.glob('samtools/win32/*.h'))], + 'install_requires' : ['cython>=0.17',], + 'package_data' : { '' : ['*.pxd', '*.h'], }, # do not pack in order to permit linking to csamtools.so 'zip_safe' :False, 'use_2to3': True, } -if sys.version_info[0] < 3: - metadata['py_modules'].append("pysam/namedtuple") - if __name__=='__main__': dist = setup(**metadata) - diff --git a/tabix/bedidx.c b/tabix/bedidx.c new file mode 100644 index 0000000..722877d --- /dev/null +++ b/tabix/bedidx.c @@ -0,0 +1,156 @@ +#include +#include +#include +#include +#include + +#include "ksort.h" +KSORT_INIT_GENERIC(uint64_t) + +#include "kseq.h" +KSTREAM_INIT(gzFile, gzread, 8192) + +typedef struct { + int n, m; + uint64_t *a; + int *idx; +} bed_reglist_t; + +#include "khash.h" +KHASH_MAP_INIT_STR(reg, bed_reglist_t) + +#define LIDX_SHIFT 13 + +typedef kh_reg_t reghash_t; + +int *bed_index_core(int n, uint64_t *a, int *n_idx) +{ + int i, j, m, *idx; + m = *n_idx = 0; idx = 0; + for (i = 0; i < n; ++i) { + int beg, end; + beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT; + if (m < end + 1) { + int oldm = m; + m = end + 1; + kroundup32(m); + idx = realloc(idx, m * sizeof(int)); + for (j = oldm; j < m; ++j) idx[j] = -1; + } + if (beg == end) { + if (idx[beg] < 0) idx[beg] = i; + } else { + for (j = beg; j <= end; ++j) + if (idx[j] < 0) idx[j] = i; + } + *n_idx = end + 1; + } + return idx; +} + +void bed_index(void *_h) +{ + reghash_t *h = (reghash_t*)_h; + khint_t k; + for (k = 0; k < kh_end(h); ++k) { + if (kh_exist(h, k)) { + bed_reglist_t *p = &kh_val(h, k); + if (p->idx) free(p->idx); + ks_introsort(uint64_t, p->n, p->a); + p->idx = bed_index_core(p->n, p->a, &p->m); + } + } +} + +int bed_overlap_core(const bed_reglist_t *p, int beg, int end) +{ + int i, min_off; + if (p->n == 0) return 0; + min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT]; + if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here + int n = beg>>LIDX_SHIFT; + if (n > p->n) n = p->n; + for (i = n - 1; i >= 0; --i) + if (p->idx[i] >= 0) break; + min_off = i >= 0? p->idx[i] : 0; + } + for (i = min_off; i < p->n; ++i) { + if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed + if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end) + return 1; // find the overlap; return + } + return 0; +} + +int bed_overlap(const void *_h, const char *chr, int beg, int end) +{ + const reghash_t *h = (const reghash_t*)_h; + khint_t k; + if (!h) return 0; + k = kh_get(reg, h, chr); + if (k == kh_end(h)) return 0; + return bed_overlap_core(&kh_val(h, k), beg, end); +} + +void *bed_read(const char *fn) +{ + reghash_t *h = kh_init(reg); + gzFile fp; + kstream_t *ks; + int dret; + kstring_t *str; + // read the list + fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); + if (fp == 0) return 0; + str = calloc(1, sizeof(kstring_t)); + ks = ks_init(fp); + while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name + int beg = -1, end = -1; + bed_reglist_t *p; + khint_t k = kh_get(reg, h, str->s); + if (k == kh_end(h)) { // absent from the hash table + int ret; + char *s = strdup(str->s); + k = kh_put(reg, h, s, &ret); + memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); + } + p = &kh_val(h, k); + if (dret != '\n') { // if the lines has other characters + if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) { + beg = atoi(str->s); // begin + if (dret != '\n') { + if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) + end = atoi(str->s); // end + } + } + } + if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line + if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column + if (beg >= 0 && end > beg) { + if (p->n == p->m) { + p->m = p->m? p->m<<1 : 4; + p->a = realloc(p->a, p->m * 8); + } + p->a[p->n++] = (uint64_t)beg<<32 | end; + } + } + ks_destroy(ks); + gzclose(fp); + free(str->s); free(str); + bed_index(h); + return h; +} + +void bed_destroy(void *_h) +{ + reghash_t *h = (reghash_t*)_h; + khint_t k; + for (k = 0; k < kh_end(h); ++k) { + if (kh_exist(h, k)) { + free(kh_val(h, k).a); + free(kh_val(h, k).idx); + free((char*)kh_key(h, k)); + } + } + kh_destroy(reg, h); +} diff --git a/tabix/bgzf.c b/tabix/bgzf.c new file mode 100644 index 0000000..3bea718 --- /dev/null +++ b/tabix/bgzf.c @@ -0,0 +1,555 @@ +/* The MIT License + + Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology + 2011 Attractive Chaos + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +#include +#include +#include +#include +#include +#include +#include "bgzf.h" + +#ifdef _USE_KNETFILE +#include "knetfile.h" +typedef knetFile *_bgzf_file_t; +#define _bgzf_open(fn, mode) knet_open(fn, mode) +#define _bgzf_dopen(fp, mode) knet_dopen(fp, mode) +#define _bgzf_close(fp) knet_close(fp) +#define _bgzf_fileno(fp) ((fp)->fd) +#define _bgzf_tell(fp) knet_tell(fp) +#define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence) +#define _bgzf_read(fp, buf, len) knet_read(fp, buf, len) +#define _bgzf_write(fp, buf, len) knet_write(fp, buf, len) +#else // ~defined(_USE_KNETFILE) +#if defined(_WIN32) || defined(_MSC_VER) +#define ftello(fp) ftell(fp) +#define fseeko(fp, offset, whence) fseek(fp, offset, whence) +#else // ~defined(_WIN32) +extern off_t ftello(FILE *stream); +extern int fseeko(FILE *stream, off_t offset, int whence); +#endif // ~defined(_WIN32) +typedef FILE *_bgzf_file_t; +#define _bgzf_open(fn, mode) fopen(fn, mode) +#define _bgzf_dopen(fp, mode) fdopen(fp, mode) +#define _bgzf_close(fp) fclose(fp) +#define _bgzf_fileno(fp) fileno(fp) +#define _bgzf_tell(fp) ftello(fp) +#define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence) +#define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp) +#define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp) +#endif // ~define(_USE_KNETFILE) + +#define BLOCK_HEADER_LENGTH 18 +#define BLOCK_FOOTER_LENGTH 8 + +/* BGZF/GZIP header (speciallized from RFC 1952; little endian): + +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ + | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN| + +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ +*/ +static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; + +#ifdef BGZF_CACHE +typedef struct { + int size; + uint8_t *block; + int64_t end_offset; +} cache_t; +#include "khash.h" +KHASH_MAP_INIT_INT64(cache, cache_t) +#endif + +static inline void packInt16(uint8_t *buffer, uint16_t value) +{ + buffer[0] = value; + buffer[1] = value >> 8; +} + +static inline int unpackInt16(const uint8_t *buffer) +{ + return buffer[0] | buffer[1] << 8; +} + +static inline void packInt32(uint8_t *buffer, uint32_t value) +{ + buffer[0] = value; + buffer[1] = value >> 8; + buffer[2] = value >> 16; + buffer[3] = value >> 24; +} + +static BGZF *bgzf_read_init() +{ + BGZF *fp; + fp = calloc(1, sizeof(BGZF)); + fp->open_mode = 'r'; + fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE); + fp->compressed_block = malloc(BGZF_BLOCK_SIZE); +#ifdef BGZF_CACHE + fp->cache = kh_init(cache); +#endif + return fp; +} + +static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level +{ + BGZF *fp; + fp = calloc(1, sizeof(BGZF)); + fp->open_mode = 'w'; + fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE); + fp->compressed_block = malloc(BGZF_BLOCK_SIZE); + fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1 + if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION; + return fp; +} +// get the compress level from the mode string +static int mode2level(const char *__restrict mode) +{ + int i, compress_level = -1; + for (i = 0; mode[i]; ++i) + if (mode[i] >= '0' && mode[i] <= '9') break; + if (mode[i]) compress_level = (int)mode[i] - '0'; + if (strchr(mode, 'u')) compress_level = 0; + return compress_level; +} + +BGZF *bgzf_open(const char *path, const char *mode) +{ + BGZF *fp = 0; + if (strchr(mode, 'r') || strchr(mode, 'R')) { + _bgzf_file_t fpr; + if ((fpr = _bgzf_open(path, "r")) == 0) return 0; + fp = bgzf_read_init(); + fp->fp = fpr; + } else if (strchr(mode, 'w') || strchr(mode, 'W')) { + FILE *fpw; + if ((fpw = fopen(path, "w")) == 0) return 0; + fp = bgzf_write_init(mode2level(mode)); + fp->fp = fpw; + } + return fp; +} + +BGZF *bgzf_dopen(int fd, const char *mode) +{ + BGZF *fp = 0; + if (strchr(mode, 'r') || strchr(mode, 'R')) { + _bgzf_file_t fpr; + if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0; + fp = bgzf_read_init(); + fp->fp = fpr; + } else if (strchr(mode, 'w') || strchr(mode, 'W')) { + FILE *fpw; + if ((fpw = fdopen(fd, "w")) == 0) return 0; + fp = bgzf_write_init(mode2level(mode)); + fp->fp = fpw; + } + return fp; +} + +// Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length. +static int deflate_block(BGZF *fp, int block_length) +{ + uint8_t *buffer = fp->compressed_block; + int buffer_size = BGZF_BLOCK_SIZE; + int input_length = block_length; + int compressed_length = 0; + int remaining; + uint32_t crc; + + assert(block_length <= BGZF_BLOCK_SIZE); // guaranteed by the caller + memcpy(buffer, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block + while (1) { // loop to retry for blocks that do not compress enough + int status; + z_stream zs; + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = fp->uncompressed_block; + zs.avail_in = input_length; + zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH]; + zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; + status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY); // -15 to disable zlib header/footer + if (status != Z_OK) { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + status = deflate(&zs, Z_FINISH); + if (status != Z_STREAM_END) { // not compressed enough + deflateEnd(&zs); // reset the stream + if (status == Z_OK) { // reduce the size and recompress + input_length -= 1024; + assert(input_length > 0); // logically, this should not happen + continue; + } + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + if (deflateEnd(&zs) != Z_OK) { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + compressed_length = zs.total_out; + compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; + assert(compressed_length <= BGZF_BLOCK_SIZE); + break; + } + + assert(compressed_length > 0); + packInt16((uint8_t*)&buffer[16], compressed_length - 1); // write the compressed_length; -1 to fit 2 bytes + crc = crc32(0L, NULL, 0L); + crc = crc32(crc, fp->uncompressed_block, input_length); + packInt32((uint8_t*)&buffer[compressed_length-8], crc); + packInt32((uint8_t*)&buffer[compressed_length-4], input_length); + + remaining = block_length - input_length; + if (remaining > 0) { + assert(remaining <= input_length); + memcpy(fp->uncompressed_block, fp->uncompressed_block + input_length, remaining); + } + fp->block_offset = remaining; + return compressed_length; +} + +// Inflate the block in fp->compressed_block into fp->uncompressed_block +static int inflate_block(BGZF* fp, int block_length) +{ + z_stream zs; + zs.zalloc = NULL; + zs.zfree = NULL; + zs.next_in = fp->compressed_block + 18; + zs.avail_in = block_length - 16; + zs.next_out = fp->uncompressed_block; + zs.avail_out = BGZF_BLOCK_SIZE; + + if (inflateInit2(&zs, -15) != Z_OK) { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + if (inflate(&zs, Z_FINISH) != Z_STREAM_END) { + inflateEnd(&zs); + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + if (inflateEnd(&zs) != Z_OK) { + fp->errcode |= BGZF_ERR_ZLIB; + return -1; + } + return zs.total_out; +} + +static int check_header(const uint8_t *header) +{ + return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0 + && unpackInt16((uint8_t*)&header[10]) == 6 + && header[12] == 'B' && header[13] == 'C' + && unpackInt16((uint8_t*)&header[14]) == 2); +} + +#ifdef BGZF_CACHE +static void free_cache(BGZF *fp) +{ + khint_t k; + khash_t(cache) *h = (khash_t(cache)*)fp->cache; + if (fp->open_mode != 'r') return; + for (k = kh_begin(h); k < kh_end(h); ++k) + if (kh_exist(h, k)) free(kh_val(h, k).block); + kh_destroy(cache, h); +} + +static int load_block_from_cache(BGZF *fp, int64_t block_address) +{ + khint_t k; + cache_t *p; + khash_t(cache) *h = (khash_t(cache)*)fp->cache; + k = kh_get(cache, h, block_address); + if (k == kh_end(h)) return 0; + p = &kh_val(h, k); + if (fp->block_length != 0) fp->block_offset = 0; + fp->block_address = block_address; + fp->block_length = p->size; + memcpy(fp->uncompressed_block, p->block, BGZF_BLOCK_SIZE); + _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET); + return p->size; +} + +static void cache_block(BGZF *fp, int size) +{ + int ret; + khint_t k; + cache_t *p; + khash_t(cache) *h = (khash_t(cache)*)fp->cache; + if (BGZF_BLOCK_SIZE >= fp->cache_size) return; + if ((kh_size(h) + 1) * BGZF_BLOCK_SIZE > fp->cache_size) { + /* A better way would be to remove the oldest block in the + * cache, but here we remove a random one for simplicity. This + * should not have a big impact on performance. */ + for (k = kh_begin(h); k < kh_end(h); ++k) + if (kh_exist(h, k)) break; + if (k < kh_end(h)) { + free(kh_val(h, k).block); + kh_del(cache, h, k); + } + } + k = kh_put(cache, h, fp->block_address, &ret); + if (ret == 0) return; // if this happens, a bug! + p = &kh_val(h, k); + p->size = fp->block_length; + p->end_offset = fp->block_address + size; + p->block = malloc(BGZF_BLOCK_SIZE); + memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_BLOCK_SIZE); +} +#else +static void free_cache(BGZF *fp) {} +static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;} +static void cache_block(BGZF *fp, int size) {} +#endif + +int bgzf_read_block(BGZF *fp) +{ + uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; + int count, size = 0, block_length, remaining; + int64_t block_address; + block_address = _bgzf_tell((_bgzf_file_t)fp->fp); + if (load_block_from_cache(fp, block_address)) return 0; + count = _bgzf_read(fp->fp, header, sizeof(header)); + if (count == 0) { // no data read + fp->block_length = 0; + return 0; + } + if (count != sizeof(header) || !check_header(header)) { + fp->errcode |= BGZF_ERR_HEADER; + return -1; + } + size = count; + block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" + compressed_block = (uint8_t*)fp->compressed_block; + memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); + remaining = block_length - BLOCK_HEADER_LENGTH; + count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); + if (count != remaining) { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + size += count; + if ((count = inflate_block(fp, block_length)) < 0) return -1; + if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek. + fp->block_address = block_address; + fp->block_length = count; + cache_block(fp, size); + return 0; +} + +ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length) +{ + ssize_t bytes_read = 0; + uint8_t *output = data; + if (length <= 0) return 0; + assert(fp->open_mode == 'r'); + while (bytes_read < length) { + int copy_length, available = fp->block_length - fp->block_offset; + uint8_t *buffer; + if (available <= 0) { + if (bgzf_read_block(fp) != 0) return -1; + available = fp->block_length - fp->block_offset; + if (available <= 0) break; + } + copy_length = length - bytes_read < available? length - bytes_read : available; + buffer = fp->uncompressed_block; + memcpy(output, buffer + fp->block_offset, copy_length); + fp->block_offset += copy_length; + output += copy_length; + bytes_read += copy_length; + } + if (fp->block_offset == fp->block_length) { + fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); + fp->block_offset = fp->block_length = 0; + } + return bytes_read; +} + +int bgzf_flush(BGZF *fp) +{ + assert(fp->open_mode == 'w'); + while (fp->block_offset > 0) { + int block_length; + block_length = deflate_block(fp, fp->block_offset); + if (block_length < 0) return -1; + if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { + fp->errcode |= BGZF_ERR_IO; // possibly truncated file + return -1; + } + fp->block_address += block_length; + } + return 0; +} + +int bgzf_flush_try(BGZF *fp, ssize_t size) +{ + if (fp->block_offset + size > BGZF_BLOCK_SIZE) + return bgzf_flush(fp); + return -1; +} + +ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length) +{ + const uint8_t *input = data; + int block_length = BGZF_BLOCK_SIZE, bytes_written; + assert(fp->open_mode == 'w'); + input = data; + bytes_written = 0; + while (bytes_written < length) { + uint8_t* buffer = fp->uncompressed_block; + int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written; + memcpy(buffer + fp->block_offset, input, copy_length); + fp->block_offset += copy_length; + input += copy_length; + bytes_written += copy_length; + if (fp->block_offset == block_length && bgzf_flush(fp)) break; + } + return bytes_written; +} + +int bgzf_close(BGZF* fp) +{ + int ret, count, block_length; + if (fp == 0) return -1; + if (fp->open_mode == 'w') { + if (bgzf_flush(fp) != 0) return -1; + block_length = deflate_block(fp, 0); // write an empty block + count = fwrite(fp->compressed_block, 1, block_length, fp->fp); + if (fflush(fp->fp) != 0) { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + } + ret = fp->open_mode == 'w'? fclose(fp->fp) : _bgzf_close(fp->fp); + if (ret != 0) return -1; + free(fp->uncompressed_block); + free(fp->compressed_block); + free_cache(fp); + free(fp); + return 0; +} + +void bgzf_set_cache_size(BGZF *fp, int cache_size) +{ + if (fp) fp->cache_size = cache_size; +} + +int bgzf_check_EOF(BGZF *fp) +{ + static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0"; + uint8_t buf[28]; + off_t offset; + offset = _bgzf_tell((_bgzf_file_t)fp->fp); + if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0; + _bgzf_read(fp->fp, buf, 28); + _bgzf_seek(fp->fp, offset, SEEK_SET); + return (memcmp(magic, buf, 28) == 0)? 1 : 0; +} + +int64_t bgzf_seek(BGZF* fp, int64_t pos, int where) +{ + int block_offset; + int64_t block_address; + + if (fp->open_mode != 'r' || where != SEEK_SET) { + fp->errcode |= BGZF_ERR_MISUSE; + return -1; + } + block_offset = pos & 0xFFFF; + block_address = pos >> 16; + if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) { + fp->errcode |= BGZF_ERR_IO; + return -1; + } + fp->block_length = 0; // indicates current block has not been loaded + fp->block_address = block_address; + fp->block_offset = block_offset; + return 0; +} + +int bgzf_is_bgzf(const char *fn) +{ + uint8_t buf[16]; + int n; + _bgzf_file_t fp; + if ((fp = _bgzf_open(fn, "r")) == 0) return 0; + n = _bgzf_read(fp, buf, 16); + _bgzf_close(fp); + if (n != 16) return 0; + return memcmp(g_magic, buf, 16) == 0? 1 : 0; +} + +int bgzf_getc(BGZF *fp) +{ + int c; + if (fp->block_offset >= fp->block_length) { + if (bgzf_read_block(fp) != 0) return -2; /* error */ + if (fp->block_length == 0) return -1; /* end-of-file */ + } + c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; + if (fp->block_offset == fp->block_length) { + fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); + fp->block_offset = 0; + fp->block_length = 0; + } + return c; +} + +#ifndef kroundup32 +#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) +#endif + +int bgzf_getline(BGZF *fp, int delim, kstring_t *str) +{ + int l, state = 0; + unsigned char *buf = (unsigned char*)fp->uncompressed_block; + str->l = 0; + do { + if (fp->block_offset >= fp->block_length) { + if (bgzf_read_block(fp) != 0) { state = -2; break; } + if (fp->block_length == 0) { state = -1; break; } + } + for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l); + if (l < fp->block_length) state = 1; + l -= fp->block_offset; + if (str->l + l + 1 >= str->m) { + str->m = str->l + l + 2; + kroundup32(str->m); + str->s = (char*)realloc(str->s, str->m); + } + memcpy(str->s + str->l, buf + fp->block_offset, l); + str->l += l; + fp->block_offset += l + 1; + if (fp->block_offset >= fp->block_length) { + fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); + fp->block_offset = 0; + fp->block_length = 0; + } + } while (state == 0); + if (str->l == 0 && state < 0) return state; + str->s[str->l] = 0; + return str->l; +} diff --git a/tabix/bgzip.c b/tabix/bgzip.c new file mode 100644 index 0000000..5429a22 --- /dev/null +++ b/tabix/bgzip.c @@ -0,0 +1,206 @@ +/* The MIT License + + Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + THE SOFTWARE. +*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include "bgzf.h" + +static const int WINDOW_SIZE = 64 * 1024; + +static int bgzip_main_usage() +{ + fprintf(stderr, "\n"); + fprintf(stderr, "Usage: bgzip [options] [file] ...\n\n"); + fprintf(stderr, "Options: -c write on standard output, keep original files unchanged\n"); + fprintf(stderr, " -d decompress\n"); + fprintf(stderr, " -f overwrite files without asking\n"); + fprintf(stderr, " -b INT decompress at virtual file pointer INT\n"); + fprintf(stderr, " -s INT decompress INT bytes in the uncompressed file\n"); + fprintf(stderr, " -h give this help\n"); + fprintf(stderr, "\n"); + return 1; +} + +static int write_open(const char *fn, int is_forced) +{ + int fd = -1; + char c; + if (!is_forced) { + if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) { + fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn); + scanf("%c", &c); + if (c != 'Y' && c != 'y') { + fprintf(stderr, "[bgzip] not overwritten\n"); + exit(1); + } + } + } + if (fd < 0) { + if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) { + fprintf(stderr, "[bgzip] %s: Fail to write\n", fn); + exit(1); + } + } + return fd; +} + +static void fail(BGZF* fp) +{ + fprintf(stderr, "Error: %d\n", fp->errcode); + exit(1); +} + +int main(int argc, char **argv) +{ + int c, compress, pstdout, is_forced; + BGZF *fp; + void *buffer; + long start, end, size; + + compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; + while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){ + switch(c){ + case 'h': return bgzip_main_usage(); + case 'd': compress = 0; break; + case 'c': pstdout = 1; break; + case 'b': start = atol(optarg); break; + case 's': size = atol(optarg); break; + case 'f': is_forced = 1; break; + } + } + if (size >= 0) end = start + size; + if (end >= 0 && end < start) { + fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end); + return 1; + } + if (compress == 1) { + struct stat sbuf; + int f_src = fileno(stdin); + int f_dst = fileno(stdout); + + if ( argc>optind ) + { + if ( stat(argv[optind],&sbuf)<0 ) + { + fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); + return 1; + } + + if ((f_src = open(argv[optind], O_RDONLY)) < 0) { + fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); + return 1; + } + + if (pstdout) + f_dst = fileno(stdout); + else + { + char *name = malloc(strlen(argv[optind]) + 5); + strcpy(name, argv[optind]); + strcat(name, ".gz"); + f_dst = write_open(name, is_forced); + if (f_dst < 0) return 1; + free(name); + } + } + else if (!pstdout && isatty(fileno((FILE *)stdout)) ) + return bgzip_main_usage(); + + fp = bgzf_dopen(f_dst, "w"); + buffer = malloc(WINDOW_SIZE); + while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0) + if (bgzf_write(fp, buffer, c) < 0) fail(fp); + // f_dst will be closed here + if (bgzf_close(fp) < 0) fail(fp); + if (argc > optind && !pstdout) unlink(argv[optind]); + free(buffer); + close(f_src); + return 0; + } else { + struct stat sbuf; + int f_dst; + + if ( argc>optind ) + { + if ( stat(argv[optind],&sbuf)<0 ) + { + fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); + return 1; + } + char *name; + int len = strlen(argv[optind]); + if ( strcmp(argv[optind]+len-3,".gz") ) + { + fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]); + return 1; + } + fp = bgzf_open(argv[optind], "r"); + if (fp == NULL) { + fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]); + return 1; + } + + if (pstdout) { + f_dst = fileno(stdout); + } + else { + name = strdup(argv[optind]); + name[strlen(name) - 3] = '\0'; + f_dst = write_open(name, is_forced); + free(name); + } + } + else if (!pstdout && isatty(fileno((FILE *)stdin)) ) + return bgzip_main_usage(); + else + { + f_dst = fileno(stdout); + fp = bgzf_dopen(fileno(stdin), "r"); + if (fp == NULL) { + fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno)); + return 1; + } + } + buffer = malloc(WINDOW_SIZE); + if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp); + while (1) { + if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE); + else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start)); + if (c == 0) break; + if (c < 0) fail(fp); + start += c; + write(f_dst, buffer, c); + if (end >= 0 && start >= end) break; + } + free(buffer); + if (bgzf_close(fp) < 0) fail(fp); + if (!pstdout) unlink(argv[optind]); + return 0; + } +} diff --git a/tabix/index.c b/tabix/index.c new file mode 100644 index 0000000..15cd65e --- /dev/null +++ b/tabix/index.c @@ -0,0 +1,967 @@ +#include +#include +#include +#include "khash.h" +#include "ksort.h" +#include "kstring.h" +#include "bam_endian.h" +#ifdef _USE_KNETFILE +#include "knetfile.h" +#endif +#include "tabix.h" + +#define TAD_MIN_CHUNK_GAP 32768 +// 1<<14 is the size of minimum bin. +#define TAD_LIDX_SHIFT 14 + +typedef struct { + uint64_t u, v; +} pair64_t; + +#define pair64_lt(a,b) ((a).u < (b).u) +KSORT_INIT(offt, pair64_t, pair64_lt) + +typedef struct { + uint32_t m, n; + pair64_t *list; +} ti_binlist_t; + +typedef struct { + int32_t n, m; + uint64_t *offset; +} ti_lidx_t; + +KHASH_MAP_INIT_INT(i, ti_binlist_t) +KHASH_MAP_INIT_STR(s, int) + +struct __ti_index_t { + ti_conf_t conf; + int32_t n, max; + khash_t(s) *tname; + khash_t(i) **index; + ti_lidx_t *index2; +}; + +struct __ti_iter_t { + int from_first; // read from the first record; no random access + int tid, beg, end, n_off, i, finished; + uint64_t curr_off; + kstring_t str; + const ti_index_t *idx; + pair64_t *off; +}; + +typedef struct { + int tid, beg, end, bin; +} ti_intv_t; + +ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 }; +ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 }; +ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 }; +ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 }; +ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 }; + +/*************** + * read a line * + ***************/ + +/* +int ti_readline(BGZF *fp, kstring_t *str) +{ + int c, l = 0; + str->l = 0; + while ((c = bgzf_getc(fp)) >= 0 && c != '\n') { + ++l; + if (c != '\r') kputc(c, str); + } + if (c < 0 && l == 0) return -1; // end of file + return str->l; +} +*/ + +/* Below is a faster implementation largely equivalent to the one + * commented out above. */ +int ti_readline(BGZF *fp, kstring_t *str) +{ + return bgzf_getline(fp, '\n', str); +} + +/************************************* + * get the interval from a data line * + *************************************/ + +static inline int ti_reg2bin(uint32_t beg, uint32_t end) +{ + --end; + if (beg>>14 == end>>14) return 4681 + (beg>>14); + if (beg>>17 == end>>17) return 585 + (beg>>17); + if (beg>>20 == end>>20) return 73 + (beg>>20); + if (beg>>23 == end>>23) return 9 + (beg>>23); + if (beg>>26 == end>>26) return 1 + (beg>>26); + return 0; +} + +static int get_tid(ti_index_t *idx, const char *ss) +{ + khint_t k; + int tid; + k = kh_get(s, idx->tname, ss); + if (k == kh_end(idx->tname)) { // a new target sequence + int ret, size; + // update idx->n, ->max, ->index and ->index2 + if (idx->n == idx->max) { + idx->max = idx->max? idx->max<<1 : 8; + idx->index = realloc(idx->index, idx->max * sizeof(void*)); + idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t)); + } + memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t)); + idx->index[idx->n++] = kh_init(i); + // update ->tname + tid = size = kh_size(idx->tname); + k = kh_put(s, idx->tname, strdup(ss), &ret); + kh_value(idx->tname, k) = size; + assert(idx->n == kh_size(idx->tname)); + } else tid = kh_value(idx->tname, k); + return tid; +} + +int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv) +{ + int i, b = 0, id = 1, ncols = 0; + char *s; + intv->ss = intv->se = 0; intv->beg = intv->end = -1; + for (i = 0; i <= len; ++i) { + if (line[i] == '\t' || line[i] == 0) { + ++ncols; + if (id == conf->sc) { + intv->ss = line + b; intv->se = line + i; + } else if (id == conf->bc) { + // here ->beg is 0-based. + intv->beg = intv->end = strtol(line + b, &s, 0); + if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg; + else ++intv->end; + if (intv->beg < 0) intv->beg = 0; + if (intv->end < 1) intv->end = 1; + } else { + if ((conf->preset&0xffff) == TI_PRESET_GENERIC) { + if (id == conf->ec) intv->end = strtol(line + b, &s, 0); + } else if ((conf->preset&0xffff) == TI_PRESET_SAM) { + if (id == 6) { // CIGAR + int l = 0, op; + char *t; + for (s = line + b; s < line + i;) { + long x = strtol(s, &t, 10); + op = toupper(*t); + if (op == 'M' || op == 'D' || op == 'N') l += x; + s = t + 1; + } + if (l == 0) l = 1; + intv->end = intv->beg + l; + } + } else if ((conf->preset&0xffff) == TI_PRESET_VCF) { + // FIXME: the following is NOT tested and is likely to be buggy + if (id == 4) { + if (b < i) intv->end = intv->beg + (i - b); + } else if (id == 8) { // look for "END=" + int c = line[i]; + line[i] = 0; + s = strstr(line + b, "END="); + if (s == line + b) s += 4; + else if (s) { + s = strstr(line + b, ";END="); + if (s) s += 5; + } + if (s) intv->end = strtol(s, &s, 0); + line[i] = c; + } + } + } + b = i + 1; + ++id; + } + } +/* + if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) { + if (ncols == 1) fprintf(stderr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line); + else fprintf(stderr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line); + exit(1); + } +*/ + if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1; + return 0; +} + +static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv) +{ + ti_interval_t x; + intv->tid = intv->beg = intv->end = intv->bin = -1; + if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) { + int c = *x.se; + *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c; + intv->beg = x.beg; intv->end = x.end; + intv->bin = ti_reg2bin(intv->beg, intv->end); + return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1; + } else { + fprintf(stderr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s); + return -1; + } +} + +/************ + * indexing * + ************/ + +// requirement: len <= LEN_MASK +static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end) +{ + khint_t k; + ti_binlist_t *l; + int ret; + k = kh_put(i, h, bin, &ret); + l = &kh_value(h, k); + if (ret) { // not present + l->m = 1; l->n = 0; + l->list = (pair64_t*)calloc(l->m, 16); + } + if (l->n == l->m) { + l->m <<= 1; + l->list = (pair64_t*)realloc(l->list, l->m * 16); + } + l->list[l->n].u = beg; l->list[l->n++].v = end; +} + +static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset) +{ + int i, beg, end; + beg = _beg >> TAD_LIDX_SHIFT; + end = (_end - 1) >> TAD_LIDX_SHIFT; + if (index2->m < end + 1) { + int old_m = index2->m; + index2->m = end + 1; + kroundup32(index2->m); + index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8); + memset(index2->offset + old_m, 0, 8 * (index2->m - old_m)); + } + if (beg == end) { + if (index2->offset[beg] == 0) index2->offset[beg] = offset; + } else { + for (i = beg; i <= end; ++i) + if (index2->offset[i] == 0) index2->offset[i] = offset; + } + if (index2->n < end + 1) index2->n = end + 1; + return (uint64_t)beg<<32 | end; +} + +static void merge_chunks(ti_index_t *idx) +{ + khash_t(i) *index; + int i, l, m; + khint_t k; + for (i = 0; i < idx->n; ++i) { + index = idx->index[i]; + for (k = kh_begin(index); k != kh_end(index); ++k) { + ti_binlist_t *p; + if (!kh_exist(index, k)) continue; + p = &kh_value(index, k); + m = 0; + for (l = 1; l < p->n; ++l) { + if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v; + else p->list[++m] = p->list[l]; + } // ~for(l) + p->n = m + 1; + } // ~for(k) + } // ~for(i) +} + +static void fill_missing(ti_index_t *idx) +{ + int i, j; + for (i = 0; i < idx->n; ++i) { + ti_lidx_t *idx2 = &idx->index2[i]; + for (j = 1; j < idx2->n; ++j) + if (idx2->offset[j] == 0) + idx2->offset[j] = idx2->offset[j-1]; + } +} + +ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf) +{ + int ret; + ti_index_t *idx; + uint32_t last_bin, save_bin; + int32_t last_coor, last_tid, save_tid; + uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp; + kstring_t *str; + + str = calloc(1, sizeof(kstring_t)); + + idx = (ti_index_t*)calloc(1, sizeof(ti_index_t)); + idx->conf = *conf; + idx->n = idx->max = 0; + idx->tname = kh_init(s); + idx->index = 0; + idx->index2 = 0; + + save_bin = save_tid = last_tid = last_bin = 0xffffffffu; + save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu; + while ((ret = ti_readline(fp, str)) >= 0) { + ti_intv_t intv; + ++lineno; + if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) { + last_off = bgzf_tell(fp); + continue; + } + get_intv(idx, str, &intv); + if ( intv.beg<0 || intv.end<0 ) + { + fprintf(stderr,"[ti_index_core] the indexes overlap or are out of bounds\n"); + exit(1); + } + if (last_tid != intv.tid) { // change of chromosomes + if (last_tid>intv.tid ) + { + fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1); + exit(1); + } + last_tid = intv.tid; + last_bin = 0xffffffffu; + } else if (last_coor > intv.beg) { + fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno); + exit(1); + } + tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off); + if (last_off == 0) offset0 = tmp; + if (intv.bin != last_bin) { // then possibly write the binning index + if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record + insert_offset(idx->index[save_tid], save_bin, save_off, last_off); + save_off = last_off; + save_bin = last_bin = intv.bin; + save_tid = intv.tid; + if (save_tid < 0) break; + } + if (bgzf_tell(fp) <= last_off) { + fprintf(stderr, "[ti_index_core] bug in BGZF: %llx < %llx\n", + (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off); + exit(1); + } + last_off = bgzf_tell(fp); + last_coor = intv.beg; + } + if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp)); + merge_chunks(idx); + fill_missing(idx); + if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) { + int i, beg = offset0>>32, end = offset0&0xffffffffu; + for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0; + } + + free(str->s); free(str); + return idx; +} + +void ti_index_destroy(ti_index_t *idx) +{ + khint_t k; + int i; + if (idx == 0) return; + // destroy the name hash table + for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) { + if (kh_exist(idx->tname, k)) + free((char*)kh_key(idx->tname, k)); + } + kh_destroy(s, idx->tname); + // destroy the binning index + for (i = 0; i < idx->n; ++i) { + khash_t(i) *index = idx->index[i]; + ti_lidx_t *index2 = idx->index2 + i; + for (k = kh_begin(index); k != kh_end(index); ++k) { + if (kh_exist(index, k)) + free(kh_value(index, k).list); + } + kh_destroy(i, index); + free(index2->offset); + } + free(idx->index); + // destroy the linear index + free(idx->index2); + free(idx); +} + +/****************** + * index file I/O * + ******************/ + +void ti_index_save(const ti_index_t *idx, BGZF *fp) +{ + int32_t i, size, ti_is_be; + khint_t k; + ti_is_be = bam_is_big_endian(); + bgzf_write(fp, "TBI\1", 4); + if (ti_is_be) { + uint32_t x = idx->n; + bgzf_write(fp, bam_swap_endian_4p(&x), 4); + } else bgzf_write(fp, &idx->n, 4); + assert(sizeof(ti_conf_t) == 24); + if (ti_is_be) { // write ti_conf_t; + uint32_t x[6]; + memcpy(x, &idx->conf, 24); + for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4); + } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t)); + { // write target names + char **name; + int32_t l = 0; + name = calloc(kh_size(idx->tname), sizeof(void*)); + for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) + if (kh_exist(idx->tname, k)) + name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k); + for (i = 0; i < kh_size(idx->tname); ++i) + l += strlen(name[i]) + 1; + if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4); + else bgzf_write(fp, &l, 4); + for (i = 0; i < kh_size(idx->tname); ++i) + bgzf_write(fp, name[i], strlen(name[i]) + 1); + free(name); + } + for (i = 0; i < idx->n; ++i) { + khash_t(i) *index = idx->index[i]; + ti_lidx_t *index2 = idx->index2 + i; + // write binning index + size = kh_size(index); + if (ti_is_be) { // big endian + uint32_t x = size; + bgzf_write(fp, bam_swap_endian_4p(&x), 4); + } else bgzf_write(fp, &size, 4); + for (k = kh_begin(index); k != kh_end(index); ++k) { + if (kh_exist(index, k)) { + ti_binlist_t *p = &kh_value(index, k); + if (ti_is_be) { // big endian + uint32_t x; + x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4); + x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); + for (x = 0; (int)x < p->n; ++x) { + bam_swap_endian_8p(&p->list[x].u); + bam_swap_endian_8p(&p->list[x].v); + } + bgzf_write(fp, p->list, 16 * p->n); + for (x = 0; (int)x < p->n; ++x) { + bam_swap_endian_8p(&p->list[x].u); + bam_swap_endian_8p(&p->list[x].v); + } + } else { + bgzf_write(fp, &kh_key(index, k), 4); + bgzf_write(fp, &p->n, 4); + bgzf_write(fp, p->list, 16 * p->n); + } + } + } + // write linear index (index2) + if (ti_is_be) { + int x = index2->n; + bgzf_write(fp, bam_swap_endian_4p(&x), 4); + } else bgzf_write(fp, &index2->n, 4); + if (ti_is_be) { // big endian + int x; + for (x = 0; (int)x < index2->n; ++x) + bam_swap_endian_8p(&index2->offset[x]); + bgzf_write(fp, index2->offset, 8 * index2->n); + for (x = 0; (int)x < index2->n; ++x) + bam_swap_endian_8p(&index2->offset[x]); + } else bgzf_write(fp, index2->offset, 8 * index2->n); + } +} + +static ti_index_t *ti_index_load_core(BGZF *fp) +{ + int i, ti_is_be; + char magic[4]; + ti_index_t *idx; + ti_is_be = bam_is_big_endian(); + if (fp == 0) { + fprintf(stderr, "[ti_index_load_core] fail to load index.\n"); + return 0; + } + bgzf_read(fp, magic, 4); + if (strncmp(magic, "TBI\1", 4)) { + fprintf(stderr, "[ti_index_load] wrong magic number.\n"); + return 0; + } + idx = (ti_index_t*)calloc(1, sizeof(ti_index_t)); + bgzf_read(fp, &idx->n, 4); + if (ti_is_be) bam_swap_endian_4p(&idx->n); + idx->tname = kh_init(s); + idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*)); + idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t)); + // read idx->conf + bgzf_read(fp, &idx->conf, sizeof(ti_conf_t)); + if (ti_is_be) { + bam_swap_endian_4p(&idx->conf.preset); + bam_swap_endian_4p(&idx->conf.sc); + bam_swap_endian_4p(&idx->conf.bc); + bam_swap_endian_4p(&idx->conf.ec); + bam_swap_endian_4p(&idx->conf.meta_char); + bam_swap_endian_4p(&idx->conf.line_skip); + } + { // read target names + int j, ret; + kstring_t *str; + int32_t l; + uint8_t *buf; + bgzf_read(fp, &l, 4); + if (ti_is_be) bam_swap_endian_4p(&l); + buf = calloc(l, 1); + bgzf_read(fp, buf, l); + str = calloc(1, sizeof(kstring_t)); + for (i = j = 0; i < l; ++i) { + if (buf[i] == 0) { + khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret); + kh_value(idx->tname, k) = j++; + str->l = 0; + } else kputc(buf[i], str); + } + free(str->s); free(str); free(buf); + } + for (i = 0; i < idx->n; ++i) { + khash_t(i) *index; + ti_lidx_t *index2 = idx->index2 + i; + uint32_t key, size; + khint_t k; + int j, ret; + ti_binlist_t *p; + index = idx->index[i] = kh_init(i); + // load binning index + bgzf_read(fp, &size, 4); + if (ti_is_be) bam_swap_endian_4p(&size); + for (j = 0; j < (int)size; ++j) { + bgzf_read(fp, &key, 4); + if (ti_is_be) bam_swap_endian_4p(&key); + k = kh_put(i, index, key, &ret); + p = &kh_value(index, k); + bgzf_read(fp, &p->n, 4); + if (ti_is_be) bam_swap_endian_4p(&p->n); + p->m = p->n; + p->list = (pair64_t*)malloc(p->m * 16); + bgzf_read(fp, p->list, 16 * p->n); + if (ti_is_be) { + int x; + for (x = 0; x < p->n; ++x) { + bam_swap_endian_8p(&p->list[x].u); + bam_swap_endian_8p(&p->list[x].v); + } + } + } + // load linear index + bgzf_read(fp, &index2->n, 4); + if (ti_is_be) bam_swap_endian_4p(&index2->n); + index2->m = index2->n; + index2->offset = (uint64_t*)calloc(index2->m, 8); + bgzf_read(fp, index2->offset, index2->n * 8); + if (ti_is_be) + for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]); + } + return idx; +} + +ti_index_t *ti_index_load_local(const char *fnidx) +{ + BGZF *fp; + fp = bgzf_open(fnidx, "r"); + if (fp) { + ti_index_t *idx = ti_index_load_core(fp); + bgzf_close(fp); + return idx; + } else return 0; +} + +#ifdef _USE_KNETFILE +static void download_from_remote(const char *url) +{ + const int buf_size = 1 * 1024 * 1024; + char *fn; + FILE *fp; + uint8_t *buf; + knetFile *fp_remote; + int l; + if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return; + l = strlen(url); + for (fn = (char*)url + l - 1; fn >= url; --fn) + if (*fn == '/') break; + ++fn; // fn now points to the file name + fp_remote = knet_open(url, "r"); + if (fp_remote == 0) { + fprintf(stderr, "[download_from_remote] fail to open remote file.\n"); + return; + } + if ((fp = fopen(fn, "w")) == 0) { + fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n"); + knet_close(fp_remote); + return; + } + buf = (uint8_t*)calloc(buf_size, 1); + while ((l = knet_read(fp_remote, buf, buf_size)) != 0) + fwrite(buf, 1, l, fp); + free(buf); + fclose(fp); + knet_close(fp_remote); +} +#else +static void download_from_remote(const char *url) +{ + return; +} +#endif + +static char *get_local_version(const char *fn) +{ + struct stat sbuf; + char *fnidx = (char*)calloc(strlen(fn) + 5, 1); + strcat(strcpy(fnidx, fn), ".tbi"); + if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) { + char *p, *url; + int l = strlen(fnidx); + for (p = fnidx + l - 1; p >= fnidx; --p) + if (*p == '/') break; + url = fnidx; fnidx = strdup(p + 1); + if (stat(fnidx, &sbuf) == 0) { + free(url); + return fnidx; + } + fprintf(stderr, "[%s] downloading the index file...\n", __func__); + download_from_remote(url); + free(url); + } + if (stat(fnidx, &sbuf) == 0) return fnidx; + free(fnidx); return 0; +} + +const char **ti_seqname(const ti_index_t *idx, int *n) +{ + const char **names; + khint_t k; + *n = idx->n; + names = calloc(idx->n, sizeof(void*)); + for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k) + if (kh_exist(idx->tname, k)) + names[kh_val(idx->tname, k)] = kh_key(idx->tname, k); + return names; +} + +ti_index_t *ti_index_load(const char *fn) +{ + ti_index_t *idx; + char *fname = get_local_version(fn); + if (fname == 0) return 0; + idx = ti_index_load_local(fname); + if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load the index: %s\n", fname); + free(fname); + return idx; +} + +int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx) +{ + char *fnidx; + BGZF *fp, *fpidx; + ti_index_t *idx; + if ((fp = bgzf_open(fn, "r")) == 0) { + fprintf(stderr, "[ti_index_build2] fail to open the file: %s\n", fn); + return -1; + } + idx = ti_index_core(fp, conf); + bgzf_close(fp); + if (_fnidx == 0) { + fnidx = (char*)calloc(strlen(fn) + 5, 1); + strcpy(fnidx, fn); strcat(fnidx, ".tbi"); + } else fnidx = strdup(_fnidx); + fpidx = bgzf_open(fnidx, "w"); + if (fpidx == 0) { + fprintf(stderr, "[ti_index_build2] fail to create the index file.\n"); + free(fnidx); + return -1; + } + ti_index_save(idx, fpidx); + ti_index_destroy(idx); + bgzf_close(fpidx); + free(fnidx); + return 0; +} + +int ti_index_build(const char *fn, const ti_conf_t *conf) +{ + return ti_index_build2(fn, conf, 0); +} + +/******************************************** + * parse a region in the format chr:beg-end * + ********************************************/ + +int ti_get_tid(const ti_index_t *idx, const char *name) +{ + khiter_t iter; + const khash_t(s) *h = idx->tname; + iter = kh_get(s, h, name); /* get the tid */ + if (iter == kh_end(h)) return -1; + return kh_value(h, iter); +} + +int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end) +{ + char *s, *p; + int i, l, k; + l = strlen(str); + p = s = (char*)malloc(l+1); + /* squeeze out "," */ + for (i = k = 0; i != l; ++i) + if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i]; + s[k] = 0; + for (i = 0; i != k; ++i) if (s[i] == ':') break; + s[i] = 0; + if ((*tid = ti_get_tid(idx, s)) < 0) { + free(s); + return -1; + } + if (i == k) { /* dump the whole sequence */ + *begin = 0; *end = 1<<29; free(s); + return 0; + } + for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break; + *begin = atoi(p); + if (i < k) { + p = s + i + 1; + *end = atoi(p); + } else *end = 1<<29; + if (*begin > 0) --*begin; + free(s); + if (*begin > *end) return -1; + return 0; +} + +/******************************* + * retrieve a specified region * + *******************************/ + +#define MAX_BIN 37450 // =(8^6-1)/7+1 + +static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN]) +{ + int i = 0, k; + if (beg >= end) return 0; + if (end >= 1u<<29) end = 1u<<29; + --end; + list[i++] = 0; + for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k; + for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k; + for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k; + for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k; + for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k; + return i; +} + +ti_iter_t ti_iter_first() +{ + ti_iter_t iter; + iter = calloc(1, sizeof(struct __ti_iter_t)); + iter->from_first = 1; + return iter; +} + +ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end) +{ + uint16_t *bins; + int i, n_bins, n_off; + pair64_t *off; + khint_t k; + khash_t(i) *index; + uint64_t min_off; + ti_iter_t iter = 0; + + if (beg < 0) beg = 0; + if (end < beg) return 0; + // initialize the iterator + iter = calloc(1, sizeof(struct __ti_iter_t)); + iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1; + // random access + bins = (uint16_t*)calloc(MAX_BIN, 2); + n_bins = reg2bins(beg, end, bins); + index = idx->index[tid]; + if (idx->index2[tid].n > 0) { + min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1] + : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT]; + if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4 + int n = beg>>TAD_LIDX_SHIFT; + if (n > idx->index2[tid].n) n = idx->index2[tid].n; + for (i = n - 1; i >= 0; --i) + if (idx->index2[tid].offset[i] != 0) break; + if (i >= 0) min_off = idx->index2[tid].offset[i]; + } + } else min_off = 0; // tabix 0.1.2 may produce such index files + for (i = n_off = 0; i < n_bins; ++i) { + if ((k = kh_get(i, index, bins[i])) != kh_end(index)) + n_off += kh_value(index, k).n; + } + if (n_off == 0) { + free(bins); return iter; + } + off = (pair64_t*)calloc(n_off, 16); + for (i = n_off = 0; i < n_bins; ++i) { + if ((k = kh_get(i, index, bins[i])) != kh_end(index)) { + int j; + ti_binlist_t *p = &kh_value(index, k); + for (j = 0; j < p->n; ++j) + if (p->list[j].v > min_off) off[n_off++] = p->list[j]; + } + } + if (n_off == 0) { + free(bins); free(off); return iter; + } + free(bins); + { + int l; + ks_introsort(offt, n_off, off); + // resolve completely contained adjacent blocks + for (i = 1, l = 0; i < n_off; ++i) + if (off[l].v < off[i].v) + off[++l] = off[i]; + n_off = l + 1; + // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing + for (i = 1; i < n_off; ++i) + if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u; + { // merge adjacent blocks + for (i = 1, l = 0; i < n_off; ++i) { + if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v; + else off[++l] = off[i]; + } + n_off = l + 1; + } + } + iter->n_off = n_off; iter->off = off; + return iter; +} + +const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) +{ + if (iter->finished) return 0; + if (iter->from_first) { + int ret; + if ((ret = ti_readline(fp, &iter->str)) < 0) { + iter->finished = 1; + return 0; + } else { + if (len) *len = iter->str.l; + return iter->str.s; + } + } + if (iter->n_off == 0) return 0; + while (1) { + int ret; + if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk + if (iter->i == iter->n_off - 1) break; // no more chunks + if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug + if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek + bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET); + iter->curr_off = bgzf_tell(fp); + } + ++iter->i; + } + if ((ret = ti_readline(fp, &iter->str)) >= 0) { + ti_intv_t intv; + iter->curr_off = bgzf_tell(fp); + if (iter->str.s[0] == iter->idx->conf.meta_char) continue; + get_intv((ti_index_t*)iter->idx, &iter->str, &intv); + if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed + else if (intv.end > iter->beg && iter->end > intv.beg) { + if (len) *len = iter->str.l; + return iter->str.s; + } + } else break; // end of file + } + iter->finished = 1; + return 0; +} + +void ti_iter_destroy(ti_iter_t iter) +{ + if (iter) { + free(iter->str.s); free(iter->off); + free(iter); + } +} + +int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func) +{ + ti_iter_t iter; + const char *s; + int len; + iter = ti_iter_query(idx, tid, beg, end); + while ((s = ti_iter_read(fp, iter, &len)) != 0) + func(len, s, data); + ti_iter_destroy(iter); + return 0; +} + +const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; } + +/******************* + * High-level APIs * + *******************/ + +tabix_t *ti_open(const char *fn, const char *fnidx) +{ + tabix_t *t; + BGZF *fp; + if ((fp = bgzf_open(fn, "r")) == 0) return 0; + t = calloc(1, sizeof(tabix_t)); + t->fn = strdup(fn); + if (fnidx) t->fnidx = strdup(fnidx); + t->fp = fp; + return t; +} + +void ti_close(tabix_t *t) +{ + if (t) { + bgzf_close(t->fp); + if (t->idx) ti_index_destroy(t->idx); + free(t->fn); free(t->fnidx); + free(t); + } +} + +int ti_lazy_index_load(tabix_t *t) +{ + if (t->idx == 0) { // load index + if (t->fnidx) t->idx = ti_index_load_local(t->fnidx); + else t->idx = ti_index_load(t->fn); + if (t->idx == 0) return -1; // fail to load index + } + return 0; +} + +ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end) +{ + if (tid < 0) return ti_iter_first(); + if (ti_lazy_index_load(t) != 0) return 0; + return ti_iter_query(t->idx, tid, beg, end); +} + +ti_iter_t ti_querys(tabix_t *t, const char *reg) +{ + int tid, beg, end; + if (reg == 0) return ti_iter_first(); + if (ti_lazy_index_load(t) != 0) return 0; + if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0; + return ti_iter_query(t->idx, tid, beg, end); +} + +ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end) +{ + int tid; + if (name == 0) return ti_iter_first(); + // then need to load the index + if (ti_lazy_index_load(t) != 0) return 0; + if ((tid = ti_get_tid(t->idx, name)) < 0) return 0; + return ti_iter_query(t->idx, tid, beg, end); +} + +const char *ti_read(tabix_t *t, ti_iter_t iter, int *len) +{ + return ti_iter_read(t->fp, iter, len); +} diff --git a/tabix/knetfile.c b/tabix/knetfile.c new file mode 100644 index 0000000..7c96a3e --- /dev/null +++ b/tabix/knetfile.c @@ -0,0 +1,632 @@ +/* The MIT License + + Copyright (c) 2008 Genome Research Ltd (GRL). + + Permission is hereby granted, free of charge, to any person obtaining + a copy of this software and associated documentation files (the + "Software"), to deal in the Software without restriction, including + without limitation the rights to use, copy, modify, merge, publish, + distribute, sublicense, and/or sell copies of the Software, and to + permit persons to whom the Software is furnished to do so, subject to + the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. +*/ + +/* Contact: Heng Li */ + +/* Probably I will not do socket programming in the next few years and + therefore I decide to heavily annotate this file, for Linux and + Windows as well. -lh3 */ + +#include +#include +#include +#include +#include +#include +#include +#include + +#ifdef _WIN32 +#include +#else +#include +#include +#include +#endif + +#include "knetfile.h" + +/* In winsock.h, the type of a socket is SOCKET, which is: "typedef + * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed + * integer -1. In knetfile.c, I use "int" for socket type + * throughout. This should be improved to avoid confusion. + * + * In Linux/Mac, recv() and read() do almost the same thing. You can see + * in the header file that netread() is simply an alias of read(). In + * Windows, however, they are different and using recv() is mandatory. + */ + +/* This function tests if the file handler is ready for reading (or + * writing if is_read==0). */ +static int socket_wait(int fd, int is_read) +{ + fd_set fds, *fdr = 0, *fdw = 0; + struct timeval tv; + int ret; + tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out + FD_ZERO(&fds); + FD_SET(fd, &fds); + if (is_read) fdr = &fds; + else fdw = &fds; + ret = select(fd+1, fdr, fdw, 0, &tv); +#ifndef _WIN32 + if (ret == -1) perror("select"); +#else + if (ret == 0) + fprintf(stderr, "select time-out\n"); + else if (ret == SOCKET_ERROR) + fprintf(stderr, "select: %d\n", WSAGetLastError()); +#endif + return ret; +} + +#ifndef _WIN32 +/* This function does not work with Windows due to the lack of + * getaddrinfo() in winsock. It is addapted from an example in "Beej's + * Guide to Network Programming" (http://beej.us/guide/bgnet/). */ +static int socket_connect(const char *host, const char *port) +{ +#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0) + + int on = 1, fd; + struct linger lng = { 0, 0 }; + struct addrinfo hints, *res; + memset(&hints, 0, sizeof(struct addrinfo)); + hints.ai_family = AF_UNSPEC; + hints.ai_socktype = SOCK_STREAM; + /* In Unix/Mac, getaddrinfo() is the most convenient way to get + * server information. */ + if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo"); + if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket"); + /* The following two setsockopt() are used by ftplib + * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they + * necessary. */ + if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt"); + if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt"); + if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect"); + freeaddrinfo(res); + return fd; +} +#else +/* MinGW's printf has problem with "%lld" */ +char *int64tostr(char *buf, int64_t x) +{ + int cnt; + int i = 0; + do { + buf[i++] = '0' + x % 10; + x /= 10; + } while (x); + buf[i] = 0; + for (cnt = i, i = 0; i < cnt/2; ++i) { + int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c; + } + return buf; +} + +int64_t strtoint64(const char *buf) +{ + int64_t x; + for (x = 0; *buf != '\0'; ++buf) + x = x * 10 + ((int64_t) *buf - 48); + return x; +} +/* In windows, the first thing is to establish the TCP connection. */ +int knet_win32_init() +{ + WSADATA wsaData; + return WSAStartup(MAKEWORD(2, 2), &wsaData); +} +void knet_win32_destroy() +{ + WSACleanup(); +} +/* A slightly modfied version of the following function also works on + * Mac (and presummably Linux). However, this function is not stable on + * my Mac. It sometimes works fine but sometimes does not. Therefore for + * non-Windows OS, I do not use this one. */ +static SOCKET socket_connect(const char *host, const char *port) +{ +#define __err_connect(func) \ + do { \ + fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \ + return -1; \ + } while (0) + + int on = 1; + SOCKET fd; + struct linger lng = { 0, 0 }; + struct sockaddr_in server; + struct hostent *hp = 0; + // open socket + if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket"); + if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt"); + if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt"); + // get host info + if (isalpha(host[0])) hp = gethostbyname(host); + else { + struct in_addr addr; + addr.s_addr = inet_addr(host); + hp = gethostbyaddr((char*)&addr, 4, AF_INET); + } + if (hp == 0) __err_connect("gethost"); + // connect + server.sin_addr.s_addr = *((unsigned long*)hp->h_addr); + server.sin_family= AF_INET; + server.sin_port = htons(atoi(port)); + if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect"); + // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!) + return fd; +} +#endif + +static off_t my_netread(int fd, void *buf, off_t len) +{ + off_t rest = len, curr, l = 0; + /* recv() and read() may not read the required length of data with + * one call. They have to be called repeatedly. */ + while (rest) { + if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading + curr = netread(fd, buf + l, rest); + /* According to the glibc manual, section 13.2, a zero returned + * value indicates end-of-file (EOF), which should mean that + * read() will not return zero if EOF has not been met but data + * are not immediately available. */ + if (curr == 0) break; + l += curr; rest -= curr; + } + return l; +} + +/************************* + * FTP specific routines * + *************************/ + +static int kftp_get_response(knetFile *ftp) +{ +#ifndef _WIN32 + unsigned char c; +#else + char c; +#endif + int n = 0; + char *p; + if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0; + while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O + //fputc(c, stderr); + if (n >= ftp->max_response) { + ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256; + ftp->response = realloc(ftp->response, ftp->max_response); + } + ftp->response[n++] = c; + if (c == '\n') { + if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2]) + && ftp->response[3] != '-') break; + n = 0; + continue; + } + } + if (n < 2) return -1; + ftp->response[n-2] = 0; + return strtol(ftp->response, &p, 0); +} + +static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get) +{ + if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing + netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); + return is_get? kftp_get_response(ftp) : 0; +} + +static int kftp_pasv_prep(knetFile *ftp) +{ + char *p; + int v[6]; + kftp_send_cmd(ftp, "PASV\r\n", 1); + for (p = ftp->response; *p && *p != '('; ++p); + if (*p != '(') return -1; + ++p; + sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]); + memcpy(ftp->pasv_ip, v, 4 * sizeof(int)); + ftp->pasv_port = (v[4]<<8&0xff00) + v[5]; + return 0; +} + + +static int kftp_pasv_connect(knetFile *ftp) +{ + char host[80], port[10]; + if (ftp->pasv_port == 0) { + fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n"); + return -1; + } + sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]); + sprintf(port, "%d", ftp->pasv_port); + ftp->fd = socket_connect(host, port); + if (ftp->fd == -1) return -1; + return 0; +} + +int kftp_connect(knetFile *ftp) +{ + ftp->ctrl_fd = socket_connect(ftp->host, ftp->port); + if (ftp->ctrl_fd == -1) return -1; + kftp_get_response(ftp); + kftp_send_cmd(ftp, "USER anonymous\r\n", 1); + kftp_send_cmd(ftp, "PASS kftp@\r\n", 1); + kftp_send_cmd(ftp, "TYPE I\r\n", 1); + return 0; +} + +int kftp_reconnect(knetFile *ftp) +{ + if (ftp->ctrl_fd != -1) { + netclose(ftp->ctrl_fd); + ftp->ctrl_fd = -1; + } + netclose(ftp->fd); + ftp->fd = -1; + return kftp_connect(ftp); +} + +// initialize ->type, ->host, ->retr and ->size +knetFile *kftp_parse_url(const char *fn, const char *mode) +{ + knetFile *fp; + char *p; + int l; + if (strstr(fn, "ftp://") != fn) return 0; + for (p = (char*)fn + 6; *p && *p != '/'; ++p); + if (*p != '/') return 0; + l = p - fn - 6; + fp = calloc(1, sizeof(knetFile)); + fp->type = KNF_TYPE_FTP; + fp->fd = -1; + /* the Linux/Mac version of socket_connect() also recognizes a port + * like "ftp", but the Windows version does not. */ + fp->port = strdup("21"); + fp->host = calloc(l + 1, 1); + if (strchr(mode, 'c')) fp->no_reconnect = 1; + strncpy(fp->host, fn + 6, l); + fp->retr = calloc(strlen(p) + 8, 1); + sprintf(fp->retr, "RETR %s\r\n", p); + fp->size_cmd = calloc(strlen(p) + 8, 1); + sprintf(fp->size_cmd, "SIZE %s\r\n", p); + fp->seek_offset = 0; + return fp; +} +// place ->fd at offset off +int kftp_connect_file(knetFile *fp) +{ + int ret; + long long file_size; + if (fp->fd != -1) { + netclose(fp->fd); + if (fp->no_reconnect) kftp_get_response(fp); + } + kftp_pasv_prep(fp); + kftp_send_cmd(fp, fp->size_cmd, 1); +#ifndef _WIN32 + if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 ) + { + fprintf(stderr,"[kftp_connect_file] %s\n", fp->response); + return -1; + } +#else + const char *p = fp->response; + while (*p != ' ') ++p; + while (*p < '0' || *p > '9') ++p; + file_size = strtoint64(p); +#endif + fp->file_size = file_size; + if (fp->offset>=0) { + char tmp[32]; +#ifndef _WIN32 + sprintf(tmp, "REST %lld\r\n", (long long)fp->offset); +#else + strcpy(tmp, "REST "); + int64tostr(tmp + 5, fp->offset); + strcat(tmp, "\r\n"); +#endif + kftp_send_cmd(fp, tmp, 1); + } + kftp_send_cmd(fp, fp->retr, 0); + kftp_pasv_connect(fp); + ret = kftp_get_response(fp); + if (ret != 150) { + fprintf(stderr, "[kftp_connect_file] %s\n", fp->response); + netclose(fp->fd); + fp->fd = -1; + return -1; + } + fp->is_ready = 1; + return 0; +} + + +/************************** + * HTTP specific routines * + **************************/ + +knetFile *khttp_parse_url(const char *fn, const char *mode) +{ + knetFile *fp; + char *p, *proxy, *q; + int l; + if (strstr(fn, "http://") != fn) return 0; + // set ->http_host + for (p = (char*)fn + 7; *p && *p != '/'; ++p); + l = p - fn - 7; + fp = calloc(1, sizeof(knetFile)); + fp->http_host = calloc(l + 1, 1); + strncpy(fp->http_host, fn + 7, l); + fp->http_host[l] = 0; + for (q = fp->http_host; *q && *q != ':'; ++q); + if (*q == ':') *q++ = 0; + // get http_proxy + proxy = getenv("http_proxy"); + // set ->host, ->port and ->path + if (proxy == 0) { + fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name. + fp->port = strdup(*q? q : "80"); + fp->path = strdup(*p? p : "/"); + } else { + fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy); + for (q = fp->host; *q && *q != ':'; ++q); + if (*q == ':') *q++ = 0; + fp->port = strdup(*q? q : "80"); + fp->path = strdup(fn); + } + fp->type = KNF_TYPE_HTTP; + fp->ctrl_fd = fp->fd = -1; + fp->seek_offset = 0; + return fp; +} + +int khttp_connect_file(knetFile *fp) +{ + int ret, l = 0; + char *buf, *p; + if (fp->fd != -1) netclose(fp->fd); + fp->fd = socket_connect(fp->host, fp->port); + buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough. + l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host); + l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset); + l += sprintf(buf + l, "\r\n"); + netwrite(fp->fd, buf, l); + l = 0; + while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency + if (buf[l] == '\n' && l >= 3) + if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break; + ++l; + } + buf[l] = 0; + if (l < 14) { // prematured header + netclose(fp->fd); + fp->fd = -1; + return -1; + } + ret = strtol(buf + 8, &p, 0); // HTTP return code + if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file + off_t rest = fp->offset; + while (rest) { + off_t l = rest < 0x10000? rest : 0x10000; + rest -= my_netread(fp->fd, buf, l); + } + } else if (ret != 206 && ret != 200) { + free(buf); + fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret); + netclose(fp->fd); + fp->fd = -1; + return -1; + } + free(buf); + fp->is_ready = 1; + return 0; +} + +/******************** + * Generic routines * + ********************/ + +knetFile *knet_open(const char *fn, const char *mode) +{ + knetFile *fp = 0; + if (mode[0] != 'r') { + fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n"); + return 0; + } + if (strstr(fn, "ftp://") == fn) { + fp = kftp_parse_url(fn, mode); + if (fp == 0) return 0; + if (kftp_connect(fp) == -1) { + knet_close(fp); + return 0; + } + kftp_connect_file(fp); + } else if (strstr(fn, "http://") == fn) { + fp = khttp_parse_url(fn, mode); + if (fp == 0) return 0; + khttp_connect_file(fp); + } else { // local file +#ifdef _WIN32 + /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may + * be undefined on some systems, although it is defined on my + * Mac and the Linux I have tested on. */ + int fd = open(fn, O_RDONLY | O_BINARY); +#else + int fd = open(fn, O_RDONLY); +#endif + if (fd == -1) { + perror("open"); + return 0; + } + fp = (knetFile*)calloc(1, sizeof(knetFile)); + fp->type = KNF_TYPE_LOCAL; + fp->fd = fd; + fp->ctrl_fd = -1; + } + if (fp && fp->fd == -1) { + knet_close(fp); + return 0; + } + return fp; +} + +knetFile *knet_dopen(int fd, const char *mode) +{ + knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile)); + fp->type = KNF_TYPE_LOCAL; + fp->fd = fd; + return fp; +} + +off_t knet_read(knetFile *fp, void *buf, off_t len) +{ + off_t l = 0; + if (fp->fd == -1) return 0; + if (fp->type == KNF_TYPE_FTP) { + if (fp->is_ready == 0) { + if (!fp->no_reconnect) kftp_reconnect(fp); + kftp_connect_file(fp); + } + } else if (fp->type == KNF_TYPE_HTTP) { + if (fp->is_ready == 0) + khttp_connect_file(fp); + } + if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX + off_t rest = len, curr; + while (rest) { + curr = read(fp->fd, buf + l, rest); + if (curr == 0) break; + l += curr; rest -= curr; + } + } else l = my_netread(fp->fd, buf, len); + fp->offset += l; + return l; +} + +off_t knet_seek(knetFile *fp, int64_t off, int whence) +{ + if (whence == SEEK_SET && off == fp->offset) return 0; + if (fp->type == KNF_TYPE_LOCAL) { + /* Be aware that lseek() returns the offset after seeking, + * while fseek() returns zero on success. */ + off_t offset = lseek(fp->fd, off, whence); + if (offset == -1) { + // Be silent, it is OK for knet_seek to fail when the file is streamed + // fprintf(stderr,"[knet_seek] %s\n", strerror(errno)); + return -1; + } + fp->offset = offset; + return 0; + } + else if (fp->type == KNF_TYPE_FTP) + { + if (whence==SEEK_CUR) + fp->offset += off; + else if (whence==SEEK_SET) + fp->offset = off; + else if ( whence==SEEK_END) + fp->offset = fp->file_size+off; + fp->is_ready = 0; + return 0; + } + else if (fp->type == KNF_TYPE_HTTP) + { + if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future? + fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n"); + errno = ESPIPE; + return -1; + } + if (whence==SEEK_CUR) + fp->offset += off; + else if (whence==SEEK_SET) + fp->offset = off; + fp->is_ready = 0; + return fp->offset; + } + errno = EINVAL; + fprintf(stderr,"[knet_seek] %s\n", strerror(errno)); + return -1; +} + +int knet_close(knetFile *fp) +{ + if (fp == 0) return 0; + if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific + if (fp->fd != -1) { + /* On Linux/Mac, netclose() is an alias of close(), but on + * Windows, it is an alias of closesocket(). */ + if (fp->type == KNF_TYPE_LOCAL) close(fp->fd); + else netclose(fp->fd); + } + free(fp->host); free(fp->port); + free(fp->response); free(fp->retr); free(fp->size_cmd); // FTP specific + free(fp->path); free(fp->http_host); // HTTP specific + free(fp); + return 0; +} + +#ifdef KNETFILE_MAIN +int main(void) +{ + char *buf; + knetFile *fp; + int type = 4, l; +#ifdef _WIN32 + knet_win32_init(); +#endif + buf = calloc(0x100000, 1); + if (type == 0) { + fp = knet_open("knetfile.c", "r"); + knet_seek(fp, 1000, SEEK_SET); + } else if (type == 1) { // NCBI FTP, large file + fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r"); + knet_seek(fp, 2500000000ll, SEEK_SET); + l = knet_read(fp, buf, 255); + } else if (type == 2) { + fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); + knet_seek(fp, 1000, SEEK_SET); + } else if (type == 3) { + fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r"); + knet_seek(fp, 1000, SEEK_SET); + } else if (type == 4) { + fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r"); + knet_read(fp, buf, 10000); + knet_seek(fp, 20000, SEEK_SET); + knet_seek(fp, 10000, SEEK_SET); + l = knet_read(fp, buf+10000, 10000000) + 10000; + } + if (type != 4 && type != 1) { + knet_read(fp, buf, 255); + buf[255] = 0; + printf("%s\n", buf); + } else write(fileno(stdout), buf, l); + knet_close(fp); + free(buf); + return 0; +} +#endif diff --git a/tabix/kstring.c b/tabix/kstring.c new file mode 100644 index 0000000..e0203fa --- /dev/null +++ b/tabix/kstring.c @@ -0,0 +1,165 @@ +#include +#include +#include +#include +#include +#include "kstring.h" + +int ksprintf(kstring_t *s, const char *fmt, ...) +{ + va_list ap; + int l; + va_start(ap, fmt); + l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'. + va_end(ap); + if (l + 1 > s->m - s->l) { + s->m = s->l + l + 2; + kroundup32(s->m); + s->s = (char*)realloc(s->s, s->m); + va_start(ap, fmt); + l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); + } + va_end(ap); + s->l += l; + return l; +} + +// s MUST BE a null terminated string; l = strlen(s) +int ksplit_core(char *s, int delimiter, int *_max, int **_offsets) +{ + int i, n, max, last_char, last_start, *offsets, l; + n = 0; max = *_max; offsets = *_offsets; + l = strlen(s); + +#define __ksplit_aux do { \ + if (_offsets) { \ + s[i] = 0; \ + if (n == max) { \ + max = max? max<<1 : 2; \ + offsets = (int*)realloc(offsets, sizeof(int) * max); \ + } \ + offsets[n++] = last_start; \ + } else ++n; \ + } while (0) + + for (i = 0, last_char = last_start = 0; i <= l; ++i) { + if (delimiter == 0) { + if (isspace(s[i]) || s[i] == 0) { + if (isgraph(last_char)) __ksplit_aux; // the end of a field + } else { + if (isspace(last_char) || last_char == 0) last_start = i; + } + } else { + if (s[i] == delimiter || s[i] == 0) { + if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field + } else { + if (last_char == delimiter || last_char == 0) last_start = i; + } + } + last_char = s[i]; + } + *_max = max; *_offsets = offsets; + return n; +} + +/********************** + * Boyer-Moore search * + **********************/ + +// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html +int *ksBM_prep(const uint8_t *pat, int m) +{ + int i, *suff, *prep, *bmGs, *bmBc; + prep = calloc(m + 256, 1); + bmGs = prep; bmBc = prep + m; + { // preBmBc() + for (i = 0; i < 256; ++i) bmBc[i] = m; + for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1; + } + suff = calloc(m, sizeof(int)); + { // suffixes() + int f = 0, g; + suff[m - 1] = m; + g = m - 1; + for (i = m - 2; i >= 0; --i) { + if (i > g && suff[i + m - 1 - f] < i - g) + suff[i] = suff[i + m - 1 - f]; + else { + if (i < g) g = i; + f = i; + while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g; + suff[i] = f - g; + } + } + } + { // preBmGs() + int j = 0; + for (i = 0; i < m; ++i) bmGs[i] = m; + for (i = m - 1; i >= 0; --i) + if (suff[i] == i + 1) + for (; j < m - 1 - i; ++j) + if (bmGs[j] == m) + bmGs[j] = m - 1 - i; + for (i = 0; i <= m - 2; ++i) + bmGs[m - 1 - suff[i]] = m - 1 - i; + } + free(suff); + return prep; +} + +int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches) +{ + int i, j, *prep, *bmGs, *bmBc; + int *matches = 0, mm = 0, nm = 0; + prep = _prep? _prep : ksBM_prep(pat, m); + bmGs = prep; bmBc = prep + m; + j = 0; + while (j <= n - m) { + for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i); + if (i < 0) { + if (nm == mm) { + mm = mm? mm<<1 : 1; + matches = realloc(matches, mm * sizeof(int)); + } + matches[nm++] = j; + j += bmGs[0]; + } else { + int max = bmBc[str[i+j]] - m + 1 + i; + if (max < bmGs[i]) max = bmGs[i]; + j += max; + } + } + *n_matches = nm; + if (_prep == 0) free(prep); + return matches; +} + +#ifdef KSTRING_MAIN +#include +int main() +{ + kstring_t *s; + int *fields, n, i; + s = (kstring_t*)calloc(1, sizeof(kstring_t)); + // test ksprintf() + ksprintf(s, " abcdefg: %d ", 100); + printf("'%s'\n", s->s); + // test ksplit() + fields = ksplit(s, 0, &n); + for (i = 0; i < n; ++i) + printf("field[%d] = '%s'\n", i, s->s + fields[i]); + free(s); + + { + static char *str = "abcdefgcdg"; + static char *pat = "cd"; + int n, *matches; + matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n); + printf("%d: \n", n); + for (i = 0; i < n; ++i) + printf("- %d\n", matches[i]); + free(matches); + } + return 0; +} +#endif diff --git a/tests/example_btag.bam b/tests/example_btag.bam new file mode 100644 index 0000000000000000000000000000000000000000..7cd5c0cf56267368e9ef298ec53be659a0a41be9 GIT binary patch literal 771 zcmb2|=3rp}f&Xj_PR>jW&J4vxUs9)}BqS7Y@ICqRakG(81Jk(#`_)f+l$`b47N}?o zG+XfSw8s@QGt|6pd}jpIDvxHyBBr-tzW&02BDR;AmTucR*Xo9qe5b0*ZbLz)rko{n z1y@ZxFO=!VaxlmwV(r8uI}EqYbWQ%jspE5Jm&vRh7k@;Gh)aDt7XQF)`-7R+vyz&) zg{JL2TmAmt?{~KE?|puzI`@;)iR-(C|23z}eXCxvzVMC7k-M|!NWQQ(zfql)uwnmm zlen$S`(KLHr;l*=H_8t3L+fSUnl9w=Xm;amU53^ne zKV-ENRBZ~YSr@PWUG>^VjW529mU>@Q)5H@G>w8`(XsBYW`?b5`fv;d-g1La`^U7uH zlXv)^J}jef=HB5&X5V*59?W6Be0uVsGdzh??WL!G+!uJ9{n&~hicceFpH9)nq zU9Wvmin`sIg>JT*7CapFouXS8w${aNcu=Of@Xz%5JCE&hy25+yfvR1B|DDF&#j>`O z#KkZ6J>Sw?!6O+dllNr%=R2tj<<&iU-`FZTv7EQKe*S-3w9+Ec`^~; ygy%0i?Qd|W=Iiex=?ni|e|*sU!9{_Bl8o}SdgiovueL=Tm`PNcff=0YK?DHn(pnS% literal 0 HcmV?d00001 diff --git a/tests/pysam_test.py b/tests/pysam_test.py index 3407182..c8acf83 100755 --- a/tests/pysam_test.py +++ b/tests/pysam_test.py @@ -891,6 +891,16 @@ class TestHeaderBam(TestHeaderSam): self.samfile=pysam.Samfile( "ex3.bam","rb" ) +class TestHeader1000Genomes( unittest.TestCase ): + + bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam" + + def testRead( self ): + + f = pysam.Samfile( self.bamfile, "rb" ) + data = f.header.copy() + self.assertTrue( data ) + class TestUnmappedReads(unittest.TestCase): def testSAM(self): -- 2.30.2