include pysam/ctabix.pxd
include pysam/ctabix.c
include pysam/ctabix.pyx
+include pysam/TabProxies.c
+include pysam/TabProxies.pyx
+include pysam/TabProxies.pxd
+include pysam/cvcf.pyx
+include pysam/cvcf.pxd
+include pysam/cvcf.c
include pysam/pysam_util.h
include samtools/*.h
include samtools/*/*.h
Metadata-Version: 1.1
Name: pysam
-Version: 0.4.1
+Version: 0.5
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
Metadata-Version: 1.1
Name: pysam
-Version: 0.4.1
+Version: 0.5
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
setup.cfg
setup.py
pysam/Pileup.py
+pysam/TabProxies.c
+pysam/TabProxies.pxd
+pysam/TabProxies.pyx
+pysam/VCF.py
pysam/__init__.py
pysam/csamtools.c
pysam/csamtools.pxd
pysam/ctabix.c
pysam/ctabix.pxd
pysam/ctabix.pyx
+pysam/cvcf.c
+pysam/cvcf.pxd
+pysam/cvcf.pyx
pysam/namedtuple.py
pysam/pysam_util.c
pysam/pysam_util.h
pysam.egg-info/PKG-INFO
pysam.egg-info/SOURCES.txt
pysam.egg-info/dependency_links.txt
+pysam.egg-info/not-zip-safe
pysam.egg-info/requires.txt
pysam.egg-info/top_level.txt
samtools/bam.c.pysam.c
samtools/bam2bcf.c.pysam.c
samtools/bam2bcf.h
samtools/bam2bcf_indel.c.pysam.c
+samtools/bam2depth.c.pysam.c
samtools/bam_aux.c.pysam.c
+samtools/bam_cat.c.pysam.c
samtools/bam_color.c.pysam.c
samtools/bam_endian.h
samtools/bam_import.c.pysam.c
samtools/bam_sort.c.pysam.c
samtools/bam_stat.c.pysam.c
samtools/bam_tview.c.pysam.c
+samtools/bedidx.c.pysam.c
samtools/bgzf.c.pysam.c
samtools/bgzf.h
+samtools/cut_target.c.pysam.c
samtools/errmod.c.pysam.c
samtools/errmod.h
samtools/faidx.c.pysam.c
samtools/ksort.h
samtools/kstring.c.pysam.c
samtools/kstring.h
+samtools/msvc_compat.h
+samtools/phase.c.pysam.c
samtools/pysam.h
samtools/razf.c.pysam.c
samtools/razf.h
samtools/bcftools/bcf2qcall.c.pysam.c
samtools/bcftools/bcfutils.c.pysam.c
samtools/bcftools/call1.c.pysam.c
+samtools/bcftools/em.c.pysam.c
samtools/bcftools/fet.c.pysam.c
samtools/bcftools/index.c.pysam.c
samtools/bcftools/kfunc.c.pysam.c
-samtools/bcftools/ld.c.pysam.c
+samtools/bcftools/kmin.c.pysam.c
+samtools/bcftools/kmin.h
samtools/bcftools/prob1.c.pysam.c
samtools/bcftools/prob1.h
samtools/bcftools/vcf.c.pysam.c
+samtools/misc/md5.c.pysam.c
+samtools/misc/md5.h
samtools/win32/xcurses.h
samtools/win32/zconf.h
samtools/win32/zlib.h
tabix/bam_endian.h
+tabix/bedidx.c.pysam.c
tabix/bgzf.c.pysam.c
tabix/bgzf.h
tabix/bgzip.c.pysam.c
tabix/khash.h
tabix/knetfile.c.pysam.c
tabix/knetfile.h
+tabix/kseq.h
tabix/ksort.h
tabix/kstring.c.pysam.c
tabix/kstring.h
+tabix/msvc_compat.h
tabix/pysam.h
tabix/tabix.h
tests/00README.txt
ctabix
pysam/Pileup
csamtools
+cvcf
+TabProxies
pysam/version
pysam/__init__
yield PileupSubstitution( *[x(y) for x,y in zip(conv_subst,d) ] )
except TypeError:
raise pysam.SamtoolsError( "parsing error in line: `%s`" % line)
+
+ENCODE_GENOTYPE = {
+ 'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T',
+ 'AA': 'A', 'CC': 'C', 'GG': 'G', 'TT': 'T', 'UU': 'U',
+ 'AG': 'r', 'GA': 'R',
+ 'CT': 'y', 'TC': 'Y',
+ 'AC': 'm', 'CA': 'M',
+ 'GT': 'k', 'TG': 'K',
+ 'CG': 's', 'GC': 'S',
+ 'AT': 'w', 'TA': 'W',
+ }
+
+DECODE_GENOTYPE = {
+ 'A': 'AA',
+ 'C': 'CC',
+ 'G': 'GG',
+ 'T': 'TT',
+ 'r': 'AG', 'R': 'AG',
+ 'y': 'CT', 'Y': 'CT',
+ 'm': 'AC', 'M': 'AC',
+ 'k': 'GT', 'K': 'GT',
+ 's': 'CG', 'S': 'CG',
+ 'w': 'AT', 'W': 'AT',
+ }
+
+##------------------------------------------------------------
+def encodeGenotype( code ):
+ '''encode genotypes like GG, GA into a one-letter code.
+ The returned code is lower case if code[0] < code[1], otherwise
+ it is uppercase.
+ '''
+ return ENCODE_GENOTYPE[ code.upper() ]
+
+def decodeGenotype( code ):
+ '''decode single letter genotypes like m, M into two letters.
+ This is the reverse operation to :meth:`encodeGenotype`.
+ '''
+ return DECODE_GENOTYPE[ code ]
+
+def translateIndelGenotypeFromVCF( vcf_genotypes, ref ):
+ '''translate indel from vcf to pileup format.'''
+
+ # indels
+ def getPrefix( s1, s2 ):
+ '''get common prefix of strings s1 and s2.'''
+ n = min( len( s1), len( s2 ) )
+ for x in range( n ):
+ if s1[x] != s2[x]: return s1[:x]
+ return s1[:n]
+
+ def getSuffix( s1, s2 ):
+ '''get common sufix of strings s1 and s2.'''
+ n = min( len( s1), len( s2 ) )
+ if s1[-1] != s2[-1]: return ""
+ for x in range( -2, -n - 1, -1 ):
+ if s1[x] != s2[x]: return s1[x+1:]
+ return s1[-n:]
+
+ def getGenotype( variant, ref ):
+
+ if variant == ref: return "*", 0
+
+ if len(ref) > len(variant):
+ # is a deletion
+ if ref.startswith(variant):
+ return "-%s" % ref[len(variant):], len(variant) - 1
+ elif ref.endswith( variant ):
+ return "-%s" % ref[:-len(variant)], -1
+ else:
+ prefix = getPrefix( ref, variant )
+ suffix = getSuffix( ref, variant )
+ shared = len(prefix) + len(suffix) - len(variant)
+ # print "-", prefix, suffix, ref, variant, shared, len(prefix), len(suffix), len(ref)
+ if shared < 0:
+ raise ValueError()
+ return "-%s" % ref[len(prefix):-(len(suffix)-shared)], len(prefix) - 1
+
+ elif len(ref) < len(variant):
+ # is an insertion
+ if variant.startswith(ref):
+ return "+%s" % variant[len(ref):], len(ref) - 1
+ elif variant.endswith(ref):
+ return "+%s" % variant[:len(ref)], 0
+ else:
+ prefix = getPrefix( ref, variant )
+ suffix = getSuffix( ref, variant )
+ shared = len(prefix) + len(suffix) - len(ref)
+ if shared < 0:
+ raise ValueError()
+
+ return "+%s" % variant[len(prefix):-(len(suffix)-shared)], len(prefix)
+ else:
+ assert 0, "snp?"
+
+ # in pileup, the position refers to the base
+ # after the coordinate, hence subtract 1
+ #pos -= 1
+
+ genotypes, offsets = [], []
+ is_error = True
+
+ for variant in vcf_genotypes:
+ try:
+ g, offset = getGenotype( variant, ref )
+ except ValueError:
+ break
+
+ genotypes.append( g )
+ if g != "*": offsets.append( offset )
+
+ else:
+ is_error = False
+
+ if is_error:
+ raise ValueError()
+
+ assert len(set(offsets )) == 1, "multiple offsets for indel"
+ offset = offsets[0]
+
+ genotypes = "/".join( genotypes )
+ return genotypes, offset
+
+def vcf2pileup( vcf, sample ):
+ '''convert vcf record to pileup record.'''
+
+ chromosome = vcf.contig
+ pos = vcf.pos
+ reference = vcf.ref
+ allelles = [reference] + vcf.alt
+
+ data = vcf[sample]
+
+ # get genotype
+ genotypes = data["GT"]
+ if len(genotypes) > 1:
+ raise ValueError( "only single genotype per position, %s" % (str(vcf)))
+
+ genotypes = genotypes[0]
+
+ # not a variant
+ if genotypes[0] == ".": return None
+
+ genotypes = [ allelles[int(x)] for x in genotypes if x != "/" ]
+
+ # snp_quality is "genotype quality"
+ snp_quality = consensus_quality = data.get( "GQ", [0])[0]
+ mapping_quality = vcf.info.get( "MQ", [0])[0]
+ coverage = data.get( "DP", 0)
+
+ if len(reference) > 1 or max([len(x) for x in vcf.alt] ) > 1:
+ # indel
+ genotype, offset = translateIndelGenotypeFromVCF( genotypes, reference )
+
+ return PileupIndel( chromosome,
+ pos + offset,
+ "*",
+ genotype,
+ consensus_quality,
+ snp_quality,
+ mapping_quality,
+ coverage,
+ genotype,
+ "<" * len(genotype),
+ 0,
+ 0,
+ 0 )
+
+ else:
+
+ genotype = encodeGenotype( "".join(genotypes) )
+
+
+ read_bases = ""
+ base_qualities = ""
+
+ return PileupSubstitution( chromosome, pos, reference,
+ genotype,
+ consensus_quality,
+ snp_quality,
+ mapping_quality,
+ coverage, read_bases, base_qualities )
+
+
+def iterate_from_vcf( infile, sample ):
+ '''iterate over a vcf-formatted file.
+
+ *infile* can be any iterator over a lines.
+
+ The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution`
+ or :class:`pysam.Pileup.PileupIndel`.
+
+ Positions without a snp will be skipped.
+
+ This method is wasteful and written to support same
+ legacy code that expects samtools pileup output.
+
+ Better use the vcf parser directly.
+
+ '''
+
+
+ vcf = pysam.VCF()
+ vcf.connect( infile )
+
+ if sample not in vcf.getsamples():
+ raise KeyErorr( "sample %s not vcf file" )
+
+ for row in vcf.fetch():
+ result = vcf2pileup( row, sample )
+ if result: yield result
+
--- /dev/null
+/* Generated by Cython 0.13 on Thu May 5 14:57:52 2011 */
+
+#define PY_SSIZE_T_CLEAN
+#include "Python.h"
+#ifndef Py_PYTHON_H
+ #error Python headers needed to compile C extensions, please install development version of Python.
+#else
+
+#include <stddef.h> /* For offsetof */
+#ifndef offsetof
+#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
+#endif
+
+#if !defined(WIN32) && !defined(MS_WINDOWS)
+ #ifndef __stdcall
+ #define __stdcall
+ #endif
+ #ifndef __cdecl
+ #define __cdecl
+ #endif
+ #ifndef __fastcall
+ #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
+
+#if PY_VERSION_HEX < 0x02040000
+ #define METH_COEXIST 0
+ #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
+ #define PyDict_Contains(d,o) PySequence_Contains(d,o)
+#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 PyInt_FromSsize_t(z) PyInt_FromLong(z)
+ #define PyInt_AsSsize_t(o) PyInt_AsLong(o)
+ #define PyNumber_Index(o) PyNumber_Int(o)
+ #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+ #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
+ #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+ #define PyType_Modified(t)
+
+ typedef struct {
+ void *buf;
+ PyObject *obj;
+ Py_ssize_t len;
+ Py_ssize_t itemsize;
+ int readonly;
+ int ndim;
+ char *format;
+ Py_ssize_t *shape;
+ Py_ssize_t *strides;
+ Py_ssize_t *suboffsets;
+ void *internal;
+ } Py_buffer;
+
+ #define PyBUF_SIMPLE 0
+ #define PyBUF_WRITABLE 0x0001
+ #define PyBUF_FORMAT 0x0004
+ #define PyBUF_ND 0x0008
+ #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
+ #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
+ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
+ #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
+ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+
+#endif
+
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+#else
+ #define __Pyx_BUILTIN_MODULE_NAME "builtins"
+#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_MAJOR_VERSION >= 3
+ #define PyBaseString_Type PyUnicode_Type
+ #define PyStringObject PyUnicodeObject
+ #define PyString_Type PyUnicode_Type
+ #define PyString_Check PyUnicode_Check
+ #define PyString_CheckExact PyUnicode_CheckExact
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+
+#if PY_VERSION_HEX < 0x02060000
+ #define PyBytesObject PyStringObject
+ #define PyBytes_Type PyString_Type
+ #define PyBytes_Check PyString_Check
+ #define PyBytes_CheckExact PyString_CheckExact
+ #define PyBytes_FromString PyString_FromString
+ #define PyBytes_FromStringAndSize PyString_FromStringAndSize
+ #define PyBytes_FromFormat PyString_FromFormat
+ #define PyBytes_DecodeEscape PyString_DecodeEscape
+ #define PyBytes_AsString PyString_AsString
+ #define PyBytes_AsStringAndSize PyString_AsStringAndSize
+ #define PyBytes_Size PyString_Size
+ #define PyBytes_AS_STRING PyString_AS_STRING
+ #define PyBytes_GET_SIZE PyString_GET_SIZE
+ #define PyBytes_Repr PyString_Repr
+ #define PyBytes_Concat PyString_Concat
+ #define PyBytes_ConcatAndDel PyString_ConcatAndDel
+ #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
+ #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
+#endif
+
+#ifndef PySet_CheckExact
+# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyInt_Type PyLong_Type
+ #define PyInt_Check(op) PyLong_Check(op)
+ #define PyInt_CheckExact(op) PyLong_CheckExact(op)
+ #define PyInt_FromString PyLong_FromString
+ #define PyInt_FromUnicode PyLong_FromUnicode
+ #define PyInt_FromLong PyLong_FromLong
+ #define PyInt_FromSize_t PyLong_FromSize_t
+ #define PyInt_FromSsize_t PyLong_FromSsize_t
+ #define PyInt_AsLong PyLong_AsLong
+ #define PyInt_AS_LONG PyLong_AS_LONG
+ #define PyInt_AsSsize_t PyLong_AsSsize_t
+ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
+ #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyBoolObject PyLongObject
+#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)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#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))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
+#else
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
+ #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))
+#else
+ #define __Pyx_NAMESTR(n) (n)
+ #define __Pyx_DOCSTR(n) (n)
+#endif
+
+#ifdef __cplusplus
+#define __PYX_EXTERN_C extern "C"
+#else
+#define __PYX_EXTERN_C extern
+#endif
+
+#if defined(WIN32) || defined(MS_WINDOWS)
+#define _USE_MATH_DEFINES
+#endif
+#include <math.h>
+#define __PYX_HAVE_API__TabProxies
+#include "stdlib.h"
+#include "string.h"
+#include "stdint.h"
+#include "stdio.h"
+#include "pythread.h"
+
+/* inline attribute */
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
+
+/* unused attribute */
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || defined(__INTEL_COMPILER)
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+
+typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
+
+
+/* Type Conversion Predeclarations */
+
+#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
+#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
+
+#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
+
+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*);
+
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+
+
+#ifdef __GNUC__
+/* Test for GCC > 2.95 */
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#define likely(x) __builtin_expect(!!(x), 1)
+#define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* __GNUC__ > 2 ... */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ */
+
+static PyObject *__pyx_m;
+static PyObject *__pyx_b;
+static PyObject *__pyx_empty_tuple;
+static PyObject *__pyx_empty_bytes;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+
+
+static const char *__pyx_f[] = {
+ "TabProxies.pyx",
+ "bool.pxd",
+};
+
+/* Type declarations */
+
+/* "pysam/TabProxies.pxd":42
+ * ctypedef int uint64_t
+ *
+ * cdef class TupleProxy: # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_obj_10TabProxies_TupleProxy {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
+ char *data;
+ char **fields;
+ int nfields;
+ int index;
+ int nbytes;
+ int offset;
+ int is_modified;
+};
+
+/* "pysam/TabProxies.pxd":77
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_obj_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+};
+
+/* "pysam/TabProxies.pxd":91
+ * 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;
+};
+
+/* "pysam/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 *contig;
+ char *source;
+ char *feature;
+ uint32_t start;
+ uint32_t end;
+ char *score;
+ char *strand;
+ char *frame;
+ char *attributes;
+ int hasOwnAttributes;
+};
+
+/* "pysam/TabProxies.pxd":80
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_obj_10TabProxies_BedProxy {
+ struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
+};
+
+
+/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":20
+ * return not (buffer <= p < buffer + nbytes )
+ *
+ * cdef class TupleProxy: # <<<<<<<<<<<<<<
+ * '''Proxy class for access to parsed row as a tuple.
+ *
+ */
+
+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);
+};
+static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
+
+
+/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":488
+ * self.fromDict( r )
+ *
+ * cdef class NamedTupleProxy( TupleProxy ): # <<<<<<<<<<<<<<
+ *
+ * map_key2field = {}
+ */
+
+struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+
+
+/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":573
+ * TupleProxy._setindex(self, idx, str(value) )
+ *
+ * cdef class VCFProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
+ * '''Proxy class for access to VCF fields.
+ *
+ */
+
+struct __pyx_vtabstruct_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+
+
+/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":507
+ * return f( self.fields[idx] )
+ *
+ * cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
+ * '''Proxy class for access to Bed fields.
+ *
+ */
+
+struct __pyx_vtabstruct_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
+
+
+/* "/ifs/devel/pysam/pysam/pysam/TabProxies.pyx":231
+ * return str(v)
+ *
+ * cdef class GTFProxy( TupleProxy ): # <<<<<<<<<<<<<<
+ * '''Proxy class for access to GTF fields.
+ *
+ */
+
+struct __pyx_vtabstruct_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
+
+#ifndef CYTHON_REFNANNY
+ #define CYTHON_REFNANNY 0
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+ void (*DECREF)(void*, PyObject*, int);
+ void (*GOTREF)(void*, PyObject*, int);
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+ #define __Pyx_GIVEREF(r)
+ #define __Pyx_XDECREF(r) Py_XDECREF(r)
+#endif /* CYTHON_REFNANNY */
+#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);} } while(0)
+#define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r);} } while(0)
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+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
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+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
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+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
+ const char* function_name, int kw_allowed); /*proto*/
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+static void __Pyx_RaiseDoubleKeywordsError(
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+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
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+static CYTHON_INLINE long __Pyx_NegateNonNeg(long b) { return unlikely(b < 0) ? b : !b; }
+static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
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+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
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+}
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+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
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+}
+
+#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, i) : \
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+
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
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+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
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+ Py_INCREF(r);
+ return r;
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+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
+
+#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) {
+ PyObject *r;
+ if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
+ r = PySequence_GetItem(o, i);
+ }
+ else {
+ r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ }
+ return r;
+}
+
+static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
+
+#define __Pyx_PyObject_AsDouble(obj) \
+ ((likely(PyFloat_CheckExact(obj))) ? \
+ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
+static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+
+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*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
+
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
+
+static void __Pyx_WriteUnraisable(const char *name); /*proto*/
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
+
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
+static void __Pyx_AddTraceback(const char *funcname); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+/* Module declarations from cpython.version */
+
+/* Module declarations from cpython.ref */
+
+/* Module declarations from cpython.exc */
+
+/* Module declarations from cpython.module */
+
+/* Module declarations from cpython.mem */
+
+/* Module declarations from cpython.tuple */
+
+/* Module declarations from cpython.list */
+
+/* Module declarations from libc.stdio */
+
+/* Module declarations from cpython.object */
+
+/* Module declarations from cpython.sequence */
+
+/* Module declarations from cpython.mapping */
+
+/* Module declarations from cpython.iterator */
+
+/* Module declarations from cpython.type */
+
+/* Module declarations from cpython.number */
+
+/* Module declarations from cpython.int */
+
+/* Module declarations from __builtin__ */
+
+/* Module declarations from cpython.bool */
+
+static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0;
+/* Module declarations from cpython.long */
+
+/* Module declarations from cpython.float */
+
+/* Module declarations from cpython.complex */
+
+/* Module declarations from cpython.string */
+
+/* Module declarations from cpython.unicode */
+
+/* Module declarations from cpython.dict */
+
+/* Module declarations from cpython.instance */
+
+/* Module declarations from cpython.function */
+
+/* Module declarations from cpython.method */
+
+/* Module declarations from cpython.weakref */
+
+/* Module declarations from cpython.getargs */
+
+/* Module declarations from cpython.pythread */
+
+/* Module declarations from cpython.cobject */
+
+/* Module declarations from cpython.oldbuffer */
+
+/* Module declarations from cpython.set */
+
+/* Module declarations from cpython.buffer */
+
+/* Module declarations from cpython.bytes */
+
+/* Module declarations from cpython.pycapsule */
+
+/* Module declarations from cpython */
+
+/* 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;
+static char *__pyx_f_10TabProxies_nextItem(char *); /*proto*/
+static char *__pyx_f_10TabProxies_StrOrEmpty(char *); /*proto*/
+static int __pyx_f_10TabProxies_isNew(char *, char *, size_t); /*proto*/
+#define __Pyx_MODULE_NAME "TabProxies"
+int __pyx_module_is_main_TabProxies = 0;
+
+/* Implementation of TabProxies */
+static PyObject *__pyx_builtin_ValueError;
+static PyObject *__pyx_builtin_IndexError;
+static PyObject *__pyx_builtin_StopIteration;
+static PyObject *__pyx_builtin_xrange;
+static PyObject *__pyx_builtin_TypeError;
+static PyObject *__pyx_builtin_AttributeError;
+static PyObject *__pyx_builtin_KeyError;
+static char __pyx_k_1[] = "malformatted entry at %s";
+static char __pyx_k_2[] = "";
+static char __pyx_k_3[] = "out of memory";
+static char __pyx_k_4[] = "incomplete line at %s";
+static char __pyx_k_5[] = "row too large - more than %i fields";
+static char __pyx_k_6[] = "list index out of range";
+static char __pyx_k_7[] = "\t";
+static char __pyx_k_8[] = ".";
+static char __pyx_k_9[] = "\"%s\"";
+static char __pyx_k_10[] = ";";
+static char __pyx_k_11[] = " ";
+static char __pyx_k_12[] = "\"";
+static char __pyx_k_13[] = "%s \"%s\"";
+static char __pyx_k_14[] = "%s %s";
+static char __pyx_k_15[] = "; ";
+static char __pyx_k_16[] = "'GTFProxy' has no attribute '%s'";
+static char __pyx_k_17[] = "field %s not set";
+static char __pyx_k_18[] = "bed format requires at least three columns";
+static char __pyx_k_19[] = "contig of feature.";
+static char __pyx_k_20[] = "feature name.";
+static char __pyx_k_21[] = "feature source.";
+static char __pyx_k_22[] = "feature start (in 0-based open/closed coordinates).";
+static char __pyx_k_23[] = "feature end (in 0-based open/closed coordinates).";
+static char __pyx_k_24[] = "feature score.";
+static char __pyx_k_25[] = "feature strand.";
+static char __pyx_k_26[] = "feature frame.";
+static char __pyx_k_27[] = "feature attributes (as a string).";
+static char __pyx_k_28[] = "TupleProxy._setindex (line 154)";
+static char __pyx_k_29[] = "TupleProxy.__setitem__ (line 177)";
+static char __pyx_k_30[] = "TupleProxy.__next__ (line 192)";
+static char __pyx_k_31[] = "TupleProxy.__str__ (line 202)";
+static char __pyx_k_32[] = "toDot (line 219)";
+static char __pyx_k_33[] = "quote (line 224)";
+static char __pyx_k_34[] = "GTFProxy.asDict (line 350)";
+static char __pyx_k_35[] = "GTFProxy.fromDict (line 385)";
+static char __pyx_k_36[] = "GTFProxy.invert (line 430)";
+static char __pyx_k_37[] = "GTFProxy.keys (line 441)";
+static char __pyx_k_38[] = "GTFProxy.__getattr__ (line 449)";
+static char __pyx_k_39[] = "GTFProxy.setAttribute (line 482)";
+static char __pyx_k_40[] = "NamedTupleProxy.__setattr__ (line 492)";
+static char __pyx_k_41[] = "BedProxy.__setattr__ (line 564)";
+static char __pyx_k_42[] = "VCFProxy.__setattr__ (line 608)";
+static char __pyx_k__id[] = "id";
+static char __pyx_k__alt[] = "alt";
+static char __pyx_k__end[] = "end";
+static char __pyx_k__pos[] = "pos";
+static char __pyx_k__ref[] = "ref";
+static char __pyx_k__data[] = "data";
+static char __pyx_k__info[] = "info";
+static char __pyx_k__join[] = "join";
+static char __pyx_k__keys[] = "keys";
+static char __pyx_k__name[] = "name";
+static char __pyx_k__qual[] = "qual";
+static char __pyx_k__frame[] = "frame";
+static char __pyx_k__index[] = "index";
+static char __pyx_k__items[] = "items";
+static char __pyx_k__quote[] = "quote";
+static char __pyx_k__range[] = "range";
+static char __pyx_k__score[] = "score";
+static char __pyx_k__split[] = "split";
+static char __pyx_k__start[] = "start";
+static char __pyx_k__strip[] = "strip";
+static char __pyx_k__toDot[] = "toDot";
+static char __pyx_k__types[] = "types";
+static char __pyx_k__value[] = "value";
+static char __pyx_k__asDict[] = "asDict";
+static char __pyx_k__contig[] = "contig";
+static char __pyx_k__fields[] = "fields";
+static char __pyx_k__filter[] = "filter";
+static char __pyx_k__format[] = "format";
+static char __pyx_k__invert[] = "invert";
+static char __pyx_k__nbytes[] = "nbytes";
+static char __pyx_k__offset[] = "offset";
+static char __pyx_k__source[] = "source";
+static char __pyx_k__strand[] = "strand";
+static char __pyx_k__update[] = "update";
+static char __pyx_k__xrange[] = "xrange";
+static char __pyx_k____str__[] = "__str__";
+static char __pyx_k__feature[] = "feature";
+static char __pyx_k__itemRGB[] = "itemRGB";
+static char __pyx_k__nfields[] = "nfields";
+static char __pyx_k__BedProxy[] = "BedProxy";
+static char __pyx_k__GTFProxy[] = "GTFProxy";
+static char __pyx_k__KeyError[] = "KeyError";
+static char __pyx_k__VCFProxy[] = "VCFProxy";
+static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____next__[] = "__next__";
+static char __pyx_k____test__[] = "__test__";
+static char __pyx_k__fromDict[] = "fromDict";
+static char __pyx_k__thickEnd[] = "thickEnd";
+static char __pyx_k__TypeError[] = "TypeError";
+static char __pyx_k___setindex[] = "_setindex";
+static char __pyx_k__bedfields[] = "bedfields";
+static char __pyx_k__IndexError[] = "IndexError";
+static char __pyx_k__StringType[] = "StringType";
+static char __pyx_k__TupleProxy[] = "TupleProxy";
+static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k__attributes[] = "attributes";
+static char __pyx_k__blockCount[] = "blockCount";
+static char __pyx_k__blockSizes[] = "blockSizes";
+static char __pyx_k__thickStart[] = "thickStart";
+static char __pyx_k__StringTypes[] = "StringTypes";
+static char __pyx_k____getattr__[] = "__getattr__";
+static char __pyx_k____setattr__[] = "__setattr__";
+static char __pyx_k____setitem__[] = "__setitem__";
+static char __pyx_k__blockStarts[] = "blockStarts";
+static char __pyx_k__is_modified[] = "is_modified";
+static char __pyx_k__getMaxFields[] = "getMaxFields";
+static char __pyx_k__setAttribute[] = "setAttribute";
+static char __pyx_k__StopIteration[] = "StopIteration";
+static char __pyx_k__map_key2field[] = "map_key2field";
+static char __pyx_k__AttributeError[] = "AttributeError";
+static char __pyx_k__NamedTupleProxy[] = "NamedTupleProxy";
+static char __pyx_k__hasOwnAttributes[] = "hasOwnAttributes";
+static PyObject *__pyx_kp_s_1;
+static PyObject *__pyx_kp_s_10;
+static PyObject *__pyx_kp_s_11;
+static PyObject *__pyx_kp_s_12;
+static PyObject *__pyx_kp_s_13;
+static PyObject *__pyx_kp_s_14;
+static PyObject *__pyx_kp_s_15;
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+
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+ struct __pyx_obj_10TabProxies_TupleProxy *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_10TabProxies_TupleProxy *)o);
+ p->__pyx_vtab = __pyx_vtabptr_10TabProxies_TupleProxy;
+ if (__pyx_pf_10TabProxies_10TupleProxy___cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
+}
+
+static void __pyx_tp_dealloc_10TabProxies_TupleProxy(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pf_10TabProxies_10TupleProxy___dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ (*Py_TYPE(o)->tp_free)(o);
+}
+static PyObject *__pyx_sq_item_10TabProxies_TupleProxy(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);
+ Py_DECREF(x);
+ return r;
+}
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+ if (v) {
+ return __pyx_pf_10TabProxies_10TupleProxy___setitem__(o, i, v);
+ }
+ else {
+ PyErr_Format(PyExc_NotImplementedError,
+ "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name);
+ return -1;
+ }
+}
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+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_10TabProxies_10TupleProxy___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy___next__)},
+ {0, 0, 0, 0}
+};
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+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
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+ 0, /*nb_invert*/
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+ 0, /*nb_xor*/
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+ 0, /*nb_long*/
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+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
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+ 0, /*nb_inplace_add*/
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+ 0, /*nb_inplace_multiply*/
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+ 0, /*nb_inplace_divide*/
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+ 0, /*nb_inplace_rshift*/
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+ 0, /*nb_inplace_xor*/
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+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
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+
+static PySequenceMethods __pyx_tp_as_sequence_TupleProxy = {
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+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ __pyx_sq_item_10TabProxies_TupleProxy, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
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+static PyMappingMethods __pyx_tp_as_mapping_TupleProxy = {
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+ __pyx_pf_10TabProxies_10TupleProxy___getitem__, /*mp_subscript*/
+ __pyx_mp_ass_subscript_10TabProxies_TupleProxy, /*mp_ass_subscript*/
+};
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+static PyBufferProcs __pyx_tp_as_buffer_TupleProxy = {
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+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
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+ sizeof(struct __pyx_obj_10TabProxies_TupleProxy), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_TupleProxy, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TupleProxy, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_TupleProxy, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ __pyx_pf_10TabProxies_10TupleProxy___str__, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
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+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("Proxy class for access to parsed row as a tuple.\n\n This class represents a table row for fast read-access.\n\n Access to individual fields is via the [] operator.\n \n Only read-only access is implemented.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ __pyx_pf_10TabProxies_10TupleProxy___iter__, /*tp_iter*/
+ __pyx_pf_10TabProxies_10TupleProxy___next__, /*tp_iternext*/
+ __pyx_methods_10TabProxies_TupleProxy, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_10TabProxies_TupleProxy, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
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+ 0, /*tp_version_tag*/
+ #endif
+};
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+ if (!o) return 0;
+ p = ((struct __pyx_obj_10TabProxies_GTFProxy *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_GTFProxy;
+ if (__pyx_pf_10TabProxies_8GTFProxy___cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ Py_DECREF(o); o = 0;
+ }
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+}
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+static void __pyx_tp_dealloc_10TabProxies_GTFProxy(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
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+ ++Py_REFCNT(o);
+ __pyx_pf_10TabProxies_8GTFProxy___dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ __pyx_tp_dealloc_10TabProxies_TupleProxy(o);
+}
+static PyObject *__pyx_sq_item_10TabProxies_GTFProxy(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);
+ Py_DECREF(x);
+ return r;
+}
+
+static PyObject *__pyx_tp_getattro_10TabProxies_GTFProxy(PyObject *o, PyObject *n) {
+ PyObject *v = PyObject_GenericGetAttr(o, n);
+ if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ PyErr_Clear();
+ v = __pyx_pf_10TabProxies_8GTFProxy___getattr__(o, n);
+ }
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+}
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+static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_contig(PyObject *o, void *x) {
+ return __pyx_pf_10TabProxies_8GTFProxy_6contig___get__(o);
+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pf_10TabProxies_8GTFProxy_6contig___set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
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+static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_feature(PyObject *o, void *x) {
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+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v, void *x) {
+ if (v) {
+ return __pyx_pf_10TabProxies_8GTFProxy_7feature___set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
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+}
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+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
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+}
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+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v, void *x) {
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+ return -1;
+ }
+}
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+static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_end(PyObject *o, void *x) {
+ return __pyx_pf_10TabProxies_8GTFProxy_3end___get__(o);
+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, void *x) {
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+ return __pyx_pf_10TabProxies_8GTFProxy_3end___set__(o, v);
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+}
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+static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_score(PyObject *o, void *x) {
+ return __pyx_pf_10TabProxies_8GTFProxy_5score___get__(o);
+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v, void *x) {
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+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
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+static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_strand(PyObject *o, void *x) {
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+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v, void *x) {
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+ return __pyx_pf_10TabProxies_8GTFProxy_6strand___set__(o, v);
+ }
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+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
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+ }
+}
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+static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_frame(PyObject *o, void *x) {
+ return __pyx_pf_10TabProxies_8GTFProxy_5frame___get__(o);
+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v, void *x) {
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+ return __pyx_pf_10TabProxies_8GTFProxy_5frame___set__(o, v);
+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
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+static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_attributes(PyObject *o, void *x) {
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+}
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+static int __pyx_setprop_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject *v, void *x) {
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+ }
+ else {
+ PyErr_SetString(PyExc_NotImplementedError, "__del__");
+ return -1;
+ }
+}
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+ {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_fromDict)},
+ {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_invert, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_invert)},
+ {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy_keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_keys)},
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_8GTFProxy___getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy___getattr__)},
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+ {0, 0, 0, 0}
+};
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+ {(char *)"source", __pyx_getprop_10TabProxies_8GTFProxy_source, __pyx_setprop_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_21), 0},
+ {(char *)"start", __pyx_getprop_10TabProxies_8GTFProxy_start, __pyx_setprop_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_22), 0},
+ {(char *)"end", __pyx_getprop_10TabProxies_8GTFProxy_end, __pyx_setprop_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_23), 0},
+ {(char *)"score", __pyx_getprop_10TabProxies_8GTFProxy_score, __pyx_setprop_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_24), 0},
+ {(char *)"strand", __pyx_getprop_10TabProxies_8GTFProxy_strand, __pyx_setprop_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_25), 0},
+ {(char *)"frame", __pyx_getprop_10TabProxies_8GTFProxy_frame, __pyx_setprop_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_26), 0},
+ {(char *)"attributes", __pyx_getprop_10TabProxies_8GTFProxy_attributes, __pyx_setprop_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_27), 0},
+ {0, 0, 0, 0, 0}
+};
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+static PyNumberMethods __pyx_tp_as_number_GTFProxy = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_GTFProxy = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ __pyx_sq_item_10TabProxies_GTFProxy, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_GTFProxy = {
+ 0, /*mp_length*/
+ __pyx_pf_10TabProxies_8GTFProxy___getitem__, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_GTFProxy = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("TabProxies.GTFProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_10TabProxies_GTFProxy), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_10TabProxies_GTFProxy, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_GTFProxy, /*tp_as_number*/
+ &__pyx_tp_as_sequence_GTFProxy, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_GTFProxy, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ __pyx_pf_10TabProxies_8GTFProxy___str__, /*tp_str*/
+ __pyx_tp_getattro_10TabProxies_GTFProxy, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_GTFProxy, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("Proxy class for access to GTF fields.\n\n This class represents a GTF entry for fast read-access.\n Write-access has been added as well, though some care must\n be taken. If any of the string fields (contig, source, ...)\n are set, the new value is tied to the lifetime of the\n argument that was supplied.\n\n The only exception is the attributes field when set from\n a dictionary - this field will manage its own memory.\n\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_10TabProxies_GTFProxy, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_10TabProxies_GTFProxy, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_10TabProxies_GTFProxy, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_vtable_10TabProxies_NamedTupleProxy;
+
+static PyObject *__pyx_tp_new_10TabProxies_NamedTupleProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_10TabProxies_NamedTupleProxy *p;
+ PyObject *o = __pyx_tp_new_10TabProxies_TupleProxy(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_10TabProxies_NamedTupleProxy *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+ return o;
+}
+
+static PyObject *__pyx_tp_getattro_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n) {
+ PyObject *v = PyObject_GenericGetAttr(o, n);
+ if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ PyErr_Clear();
+ v = __pyx_pf_10TabProxies_15NamedTupleProxy___getattr__(o, n);
+ }
+ return v;
+}
+
+static int __pyx_tp_setattro_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n, PyObject *v) {
+ if (v) {
+ return __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(o, n, v);
+ }
+ else {
+ if (__pyx_ptype_10TabProxies_TupleProxy->tp_setattro)
+ return __pyx_ptype_10TabProxies_TupleProxy->tp_setattro(o, n, v);
+ return PyObject_GenericSetAttr(o, n, 0);
+ }
+}
+
+static PyMethodDef __pyx_methods_10TabProxies_NamedTupleProxy[] = {
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_10TabProxies_15NamedTupleProxy___getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)},
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_NamedTupleProxy = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_NamedTupleProxy = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_NamedTupleProxy = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_NamedTupleProxy = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("TabProxies.NamedTupleProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_NamedTupleProxy, /*tp_as_number*/
+ &__pyx_tp_as_sequence_NamedTupleProxy, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_NamedTupleProxy, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ __pyx_tp_getattro_10TabProxies_NamedTupleProxy, /*tp_getattro*/
+ __pyx_tp_setattro_10TabProxies_NamedTupleProxy, /*tp_setattro*/
+ &__pyx_tp_as_buffer_NamedTupleProxy, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ 0, /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_10TabProxies_NamedTupleProxy, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_10TabProxies_NamedTupleProxy, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+static struct __pyx_vtabstruct_10TabProxies_BedProxy __pyx_vtable_10TabProxies_BedProxy;
+
+static PyObject *__pyx_tp_new_10TabProxies_BedProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_10TabProxies_BedProxy *p;
+ PyObject *o = __pyx_tp_new_10TabProxies_TupleProxy(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_10TabProxies_BedProxy *)o);
+ p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_BedProxy;
+ return o;
+}
+
+static int __pyx_tp_setattro_10TabProxies_BedProxy(PyObject *o, PyObject *n, PyObject *v) {
+ if (v) {
+ return __pyx_pf_10TabProxies_8BedProxy___setattr__(o, n, v);
+ }
+ else {
+ if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
+ return __pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro(o, n, v);
+ return PyObject_GenericSetAttr(o, n, 0);
+ }
+}
+
+static PyMethodDef __pyx_methods_10TabProxies_BedProxy[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_BedProxy = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_BedProxy = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_BedProxy = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_BedProxy = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_10TabProxies_BedProxy = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("TabProxies.BedProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_10TabProxies_BedProxy), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_BedProxy, /*tp_as_number*/
+ &__pyx_tp_as_sequence_BedProxy, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_BedProxy, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ __pyx_pf_10TabProxies_8BedProxy___str__, /*tp_str*/
+ 0, /*tp_getattro*/
+ __pyx_tp_setattro_10TabProxies_BedProxy, /*tp_setattro*/
+ &__pyx_tp_as_buffer_BedProxy, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("Proxy class for access to Bed fields.\n\n This class represents a GTF entry for fast read-access.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_10TabProxies_BedProxy, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_10TabProxies_BedProxy, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+static struct __pyx_vtabstruct_10TabProxies_VCFProxy __pyx_vtable_10TabProxies_VCFProxy;
+
+static PyObject *__pyx_tp_new_10TabProxies_VCFProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_10TabProxies_VCFProxy *p;
+ PyObject *o = __pyx_tp_new_10TabProxies_TupleProxy(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_10TabProxies_VCFProxy *)o);
+ p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_VCFProxy;
+ if (__pyx_pf_10TabProxies_8VCFProxy___cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
+}
+
+static int __pyx_tp_setattro_10TabProxies_VCFProxy(PyObject *o, PyObject *n, PyObject *v) {
+ if (v) {
+ return __pyx_pf_10TabProxies_8VCFProxy___setattr__(o, n, v);
+ }
+ else {
+ if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
+ return __pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro(o, n, v);
+ return PyObject_GenericSetAttr(o, n, 0);
+ }
+}
+
+static PyMethodDef __pyx_methods_10TabProxies_VCFProxy[] = {
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_VCFProxy = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_VCFProxy = {
+ __pyx_pf_10TabProxies_8VCFProxy___len__, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_VCFProxy = {
+ __pyx_pf_10TabProxies_8VCFProxy___len__, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_VCFProxy = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
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+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("TabProxies.VCFProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_10TabProxies_VCFProxy), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_VCFProxy, /*tp_as_number*/
+ &__pyx_tp_as_sequence_VCFProxy, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_VCFProxy, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ __pyx_tp_setattro_10TabProxies_VCFProxy, /*tp_setattro*/
+ &__pyx_tp_as_buffer_VCFProxy, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("Proxy class for access to VCF fields.\n\n The genotypes are accessed via index.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_10TabProxies_VCFProxy, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_10TabProxies_VCFProxy, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyMethodDef __pyx_methods[] = {
+ {__Pyx_NAMESTR("toDot"), (PyCFunction)__pyx_pf_10TabProxies_toDot, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_toDot)},
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+ {0, 0, 0, 0}
+};
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+#if PY_MAJOR_VERSION >= 3
+static struct PyModuleDef __pyx_moduledef = {
+ PyModuleDef_HEAD_INIT,
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+ -1, /* m_size */
+ __pyx_methods /* m_methods */,
+ NULL, /* m_reload */
+ NULL, /* m_traverse */
+ NULL, /* m_clear */
+ NULL /* m_free */
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+ {&__pyx_n_s__AttributeError, __pyx_k__AttributeError, sizeof(__pyx_k__AttributeError), 0, 0, 1, 1},
+ {&__pyx_n_s__BedProxy, __pyx_k__BedProxy, sizeof(__pyx_k__BedProxy), 0, 0, 1, 1},
+ {&__pyx_n_s__GTFProxy, __pyx_k__GTFProxy, sizeof(__pyx_k__GTFProxy), 0, 0, 1, 1},
+ {&__pyx_n_s__IndexError, __pyx_k__IndexError, sizeof(__pyx_k__IndexError), 0, 0, 1, 1},
+ {&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
+ {&__pyx_n_s__NamedTupleProxy, __pyx_k__NamedTupleProxy, sizeof(__pyx_k__NamedTupleProxy), 0, 0, 1, 1},
+ {&__pyx_n_s__StopIteration, __pyx_k__StopIteration, sizeof(__pyx_k__StopIteration), 0, 0, 1, 1},
+ {&__pyx_n_s__StringType, __pyx_k__StringType, sizeof(__pyx_k__StringType), 0, 0, 1, 1},
+ {&__pyx_n_s__StringTypes, __pyx_k__StringTypes, sizeof(__pyx_k__StringTypes), 0, 0, 1, 1},
+ {&__pyx_n_s__TupleProxy, __pyx_k__TupleProxy, sizeof(__pyx_k__TupleProxy), 0, 0, 1, 1},
+ {&__pyx_n_s__TypeError, __pyx_k__TypeError, sizeof(__pyx_k__TypeError), 0, 0, 1, 1},
+ {&__pyx_n_s__VCFProxy, __pyx_k__VCFProxy, sizeof(__pyx_k__VCFProxy), 0, 0, 1, 1},
+ {&__pyx_n_s__ValueError, __pyx_k__ValueError, sizeof(__pyx_k__ValueError), 0, 0, 1, 1},
+ {&__pyx_n_s____getattr__, __pyx_k____getattr__, sizeof(__pyx_k____getattr__), 0, 0, 1, 1},
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+ {&__pyx_n_s____next__, __pyx_k____next__, sizeof(__pyx_k____next__), 0, 0, 1, 1},
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+ {&__pyx_n_s__asDict, __pyx_k__asDict, sizeof(__pyx_k__asDict), 0, 0, 1, 1},
+ {&__pyx_n_s__attributes, __pyx_k__attributes, sizeof(__pyx_k__attributes), 0, 0, 1, 1},
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+ {&__pyx_n_s__feature, __pyx_k__feature, sizeof(__pyx_k__feature), 0, 0, 1, 1},
+ {&__pyx_n_s__fields, __pyx_k__fields, sizeof(__pyx_k__fields), 0, 0, 1, 1},
+ {&__pyx_n_s__filter, __pyx_k__filter, sizeof(__pyx_k__filter), 0, 0, 1, 1},
+ {&__pyx_n_s__format, __pyx_k__format, sizeof(__pyx_k__format), 0, 0, 1, 1},
+ {&__pyx_n_s__frame, __pyx_k__frame, sizeof(__pyx_k__frame), 0, 0, 1, 1},
+ {&__pyx_n_s__fromDict, __pyx_k__fromDict, sizeof(__pyx_k__fromDict), 0, 0, 1, 1},
+ {&__pyx_n_s__getMaxFields, __pyx_k__getMaxFields, sizeof(__pyx_k__getMaxFields), 0, 0, 1, 1},
+ {&__pyx_n_s__hasOwnAttributes, __pyx_k__hasOwnAttributes, sizeof(__pyx_k__hasOwnAttributes), 0, 0, 1, 1},
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+ {&__pyx_n_s__index, __pyx_k__index, sizeof(__pyx_k__index), 0, 0, 1, 1},
+ {&__pyx_n_s__info, __pyx_k__info, sizeof(__pyx_k__info), 0, 0, 1, 1},
+ {&__pyx_n_s__invert, __pyx_k__invert, sizeof(__pyx_k__invert), 0, 0, 1, 1},
+ {&__pyx_n_s__is_modified, __pyx_k__is_modified, sizeof(__pyx_k__is_modified), 0, 0, 1, 1},
+ {&__pyx_n_s__itemRGB, __pyx_k__itemRGB, sizeof(__pyx_k__itemRGB), 0, 0, 1, 1},
+ {&__pyx_n_s__items, __pyx_k__items, sizeof(__pyx_k__items), 0, 0, 1, 1},
+ {&__pyx_n_s__join, __pyx_k__join, sizeof(__pyx_k__join), 0, 0, 1, 1},
+ {&__pyx_n_s__keys, __pyx_k__keys, sizeof(__pyx_k__keys), 0, 0, 1, 1},
+ {&__pyx_n_s__map_key2field, __pyx_k__map_key2field, sizeof(__pyx_k__map_key2field), 0, 0, 1, 1},
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+ {&__pyx_n_s__setAttribute, __pyx_k__setAttribute, sizeof(__pyx_k__setAttribute), 0, 0, 1, 1},
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+ {&__pyx_n_s__thickEnd, __pyx_k__thickEnd, sizeof(__pyx_k__thickEnd), 0, 0, 1, 1},
+ {&__pyx_n_s__thickStart, __pyx_k__thickStart, sizeof(__pyx_k__thickStart), 0, 0, 1, 1},
+ {&__pyx_n_s__toDot, __pyx_k__toDot, sizeof(__pyx_k__toDot), 0, 0, 1, 1},
+ {&__pyx_n_s__types, __pyx_k__types, sizeof(__pyx_k__types), 0, 0, 1, 1},
+ {&__pyx_n_s__update, __pyx_k__update, sizeof(__pyx_k__update), 0, 0, 1, 1},
+ {&__pyx_n_s__value, __pyx_k__value, sizeof(__pyx_k__value), 0, 0, 1, 1},
+ {&__pyx_n_s__xrange, __pyx_k__xrange, sizeof(__pyx_k__xrange), 0, 0, 1, 1},
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+static int __Pyx_InitCachedBuiltins(void) {
+ __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_IndexError = __Pyx_GetName(__pyx_b, __pyx_n_s__IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if PY_MAJOR_VERSION >= 3
+ __pyx_builtin_xrange = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_builtin_xrange = __Pyx_GetName(__pyx_b, __pyx_n_s__xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_AttributeError = __Pyx_GetName(__pyx_b, __pyx_n_s__AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ return 0;
+ __pyx_L1_error:;
+ return -1;
+}
+
+static int __Pyx_InitGlobals(void) {
+ if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_2 = PyInt_FromLong(2); if (unlikely(!__pyx_int_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_3 = PyInt_FromLong(3); if (unlikely(!__pyx_int_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_4 = PyInt_FromLong(4); if (unlikely(!__pyx_int_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_5 = PyInt_FromLong(5); if (unlikely(!__pyx_int_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_6 = PyInt_FromLong(6); if (unlikely(!__pyx_int_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_7 = PyInt_FromLong(7); if (unlikely(!__pyx_int_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_9 = PyInt_FromLong(9); if (unlikely(!__pyx_int_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ __pyx_int_10 = PyInt_FromLong(10); if (unlikely(!__pyx_int_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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+ return 0;
+ __pyx_L1_error:;
+ return -1;
+}
+
+#if PY_MAJOR_VERSION < 3
+PyMODINIT_FUNC initTabProxies(void); /*proto*/
+PyMODINIT_FUNC initTabProxies(void)
+#else
+PyMODINIT_FUNC PyInit_TabProxies(void); /*proto*/
+PyMODINIT_FUNC PyInit_TabProxies(void)
+#endif
+{
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+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
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+ #ifdef __pyx_binding_PyCFunctionType_USED
+ if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
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+ /*--- Threads initialization code ---*/
+ #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
+ #ifdef WITH_THREAD /* Python build with threading support? */
+ PyEval_InitThreads();
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+ #endif
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+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("TabProxies"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
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+ __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);
+ #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_TabProxies) {
+ 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 ---*/
+ if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Global init code ---*/
+ /*--- Function export code ---*/
+ /*--- Type init code ---*/
+ __pyx_vtabptr_10TabProxies_TupleProxy = &__pyx_vtable_10TabProxies_TupleProxy;
+ #if PY_MAJOR_VERSION >= 3
+ __pyx_vtable_10TabProxies_TupleProxy.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_10TupleProxy_getMaxFields;
+ __pyx_vtable_10TabProxies_TupleProxy.take = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_take;
+ __pyx_vtable_10TabProxies_TupleProxy.present = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_present;
+ __pyx_vtable_10TabProxies_TupleProxy.copy = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_copy;
+ __pyx_vtable_10TabProxies_TupleProxy.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_update;
+ #else
+ *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_getMaxFields;
+ *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.take = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_take;
+ *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.present = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_present;
+ *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.copy = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_copy;
+ *(void(**)(void))&__pyx_vtable_10TabProxies_TupleProxy.update = (void(*)(void))__pyx_f_10TabProxies_10TupleProxy_update;
+ #endif
+ if (PyType_Ready(&__pyx_type_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__setitem__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__.doc = __pyx_doc_10TabProxies_10TupleProxy___setitem__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___setitem__;
+ }
+ }
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_10TabProxies_10TupleProxy___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy___next__.doc = __pyx_doc_10TabProxies_10TupleProxy___next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___next__;
+ }
+ }
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_10TabProxies_10TupleProxy___str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_10TupleProxy___str__.doc = __pyx_doc_10TabProxies_10TupleProxy___str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy___str__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_TupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "TupleProxy", (PyObject *)&__pyx_type_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 20; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_TupleProxy = &__pyx_type_10TabProxies_TupleProxy;
+ __pyx_vtabptr_10TabProxies_GTFProxy = &__pyx_vtable_10TabProxies_GTFProxy;
+ __pyx_vtable_10TabProxies_GTFProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
+ #if PY_MAJOR_VERSION >= 3
+ __pyx_vtable_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8GTFProxy_getMaxFields;
+ __pyx_vtable_10TabProxies_GTFProxy.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8GTFProxy_update;
+ #else
+ *(void(**)(void))&__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_8GTFProxy_getMaxFields;
+ *(void(**)(void))&__pyx_vtable_10TabProxies_GTFProxy.__pyx_base.update = (void(*)(void))__pyx_f_10TabProxies_8GTFProxy_update;
+ #endif
+ __pyx_type_10TabProxies_GTFProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
+ if (PyType_Ready(&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__.doc = __pyx_doc_10TabProxies_8GTFProxy___getattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8GTFProxy___getattr__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_GTFProxy.tp_dict, __pyx_vtabptr_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_GTFProxy = &__pyx_type_10TabProxies_GTFProxy;
+ __pyx_vtabptr_10TabProxies_NamedTupleProxy = &__pyx_vtable_10TabProxies_NamedTupleProxy;
+ __pyx_vtable_10TabProxies_NamedTupleProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
+ __pyx_type_10TabProxies_NamedTupleProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
+ if (PyType_Ready(&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__.doc = __pyx_doc_10TabProxies_15NamedTupleProxy___setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_NamedTupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "NamedTupleProxy", (PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_NamedTupleProxy = &__pyx_type_10TabProxies_NamedTupleProxy;
+ __pyx_vtabptr_10TabProxies_BedProxy = &__pyx_vtable_10TabProxies_BedProxy;
+ __pyx_vtable_10TabProxies_BedProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+ #if PY_MAJOR_VERSION >= 3
+ __pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8BedProxy_getMaxFields;
+ __pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8BedProxy_update;
+ #else
+ *(void(**)(void))&__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (void(*)(void))__pyx_f_10TabProxies_8BedProxy_getMaxFields;
+ *(void(**)(void))&__pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (void(*)(void))__pyx_f_10TabProxies_8BedProxy_update;
+ #endif
+ __pyx_type_10TabProxies_BedProxy.tp_base = __pyx_ptype_10TabProxies_NamedTupleProxy;
+ if (PyType_Ready(&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_BedProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_10TabProxies_8BedProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_8BedProxy___setattr__.doc = __pyx_doc_10TabProxies_8BedProxy___setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8BedProxy___setattr__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_BedProxy.tp_dict, __pyx_vtabptr_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BedProxy", (PyObject *)&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_BedProxy = &__pyx_type_10TabProxies_BedProxy;
+ __pyx_vtabptr_10TabProxies_VCFProxy = &__pyx_vtable_10TabProxies_VCFProxy;
+ __pyx_vtable_10TabProxies_VCFProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+ #if PY_MAJOR_VERSION >= 3
+ __pyx_vtable_10TabProxies_VCFProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8VCFProxy_update;
+ #else
+ *(void(**)(void))&__pyx_vtable_10TabProxies_VCFProxy.__pyx_base.__pyx_base.update = (void(*)(void))__pyx_f_10TabProxies_8VCFProxy_update;
+ #endif
+ __pyx_type_10TabProxies_VCFProxy.tp_base = __pyx_ptype_10TabProxies_NamedTupleProxy;
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+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_VCFProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_10TabProxies_8VCFProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_10TabProxies_8VCFProxy___setattr__.doc = __pyx_doc_10TabProxies_8VCFProxy___setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8VCFProxy___setattr__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_10TabProxies_VCFProxy.tp_dict, __pyx_vtabptr_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "VCFProxy", (PyObject *)&__pyx_type_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_VCFProxy = &__pyx_type_10TabProxies_VCFProxy;
+ /*--- Type import code ---*/
+ __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[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Function import code ---*/
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+ __Pyx_GOTREF(__pyx_t_1);
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+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem((PyObject *)__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict, __pyx_n_s__map_key2field, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 490; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
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+ PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)((PyObject*)&PyString_Type)));
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+ PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)((PyObject*)&PyInt_Type)));
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+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_42), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+
+ /* "/ifs/apps/apps/python-2.7.1/lib/python2.7/site-packages/Cython-0.13-py2.7-linux-x86_64.egg/Cython/Includes/cpython/type.pxd":2
+ *
+ * cdef extern from "Python.h": # <<<<<<<<<<<<<<
+ * # The C structure of the objects used to describe built-in types.
+ *
+ */
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
+ if (__pyx_m) {
+ __Pyx_AddTraceback("init TabProxies");
+ Py_DECREF(__pyx_m); __pyx_m = 0;
+ } else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_ImportError, "init TabProxies");
+ }
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ #if PY_MAJOR_VERSION < 3
+ return;
+ #else
+ return __pyx_m;
+ #endif
+}
+
+/* Runtime support code */
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+ PyObject *result;
+ result = PyObject_GetAttr(dict, name);
+ if (!result)
+ PyErr_SetObject(PyExc_NameError, name);
+ return result;
+}
+
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
+ Py_ssize_t num_expected;
+ const char *number, *more_or_less;
+
+ if (num_found < num_min) {
+ num_expected = num_min;
+ more_or_less = "at least";
+ } else {
+ num_expected = num_max;
+ more_or_less = "at most";
+ }
+ if (exact) {
+ more_or_less = "exactly";
+ }
+ number = (num_expected == 1) ? "" : "s";
+ PyErr_Format(PyExc_TypeError,
+ #if PY_VERSION_HEX < 0x02050000
+ "%s() takes %s %d positional argument%s (%d given)",
+ #else
+ "%s() takes %s %zd positional argument%s (%zd given)",
+ #endif
+ func_name, more_or_less, num_expected, number, num_found);
+}
+
+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
+ PyObject *kwdict,
+ const char* function_name,
+ int kw_allowed)
+{
+ PyObject* key = 0;
+ Py_ssize_t pos = 0;
+ while (PyDict_Next(kwdict, &pos, &key, 0)) {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
+ #endif
+ goto invalid_keyword_type;
+ }
+ if ((!kw_allowed) && unlikely(key))
+ goto invalid_keyword;
+ return 1;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ return 0;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+ return 0;
+}
+
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%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));
+ #endif
+}
+
+static int __Pyx_ParseOptionalKeywords(
+ PyObject *kwds,
+ PyObject **argnames[],
+ PyObject *kwds2,
+ PyObject *values[],
+ Py_ssize_t num_pos_args,
+ const char* function_name)
+{
+ PyObject *key = 0, *value = 0;
+ Py_ssize_t pos = 0;
+ PyObject*** name;
+ PyObject*** first_kw_arg = argnames + num_pos_args;
+
+ while (PyDict_Next(kwds, &pos, &key, &value)) {
+ name = first_kw_arg;
+ 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_CheckExact(key)) && 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) {
+ values[name-argnames] = value;
+ } else {
+ /* unexpected keyword found */
+ 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;
+ }
+ }
+ }
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ goto bad;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
+ return -1;
+}
+
+
+static double __Pyx__PyObject_AsDouble(PyObject* obj) {
+ PyObject* float_value;
+ 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)) {
+#if PY_MAJOR_VERSION >= 3
+ float_value = PyFloat_FromString(obj);
+#else
+ float_value = PyFloat_FromString(obj, 0);
+#endif
+ } else {
+ PyObject* args = PyTuple_New(1);
+ if (unlikely(!args)) goto bad;
+ PyTuple_SET_ITEM(args, 0, obj);
+ float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0);
+ PyTuple_SET_ITEM(args, 0, 0);
+ Py_DECREF(args);
+ }
+ if (likely(float_value)) {
+ double value = PyFloat_AS_DOUBLE(float_value);
+ Py_DECREF(float_value);
+ return value;
+ }
+bad:
+ return (double)-1;
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ #if PY_VERSION_HEX < 0x02050000
+ "need more than %d value%s to unpack", (int)index,
+ #else
+ "need more than %zd value%s to unpack", index,
+ #endif
+ (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ #if PY_VERSION_HEX < 0x02050000
+ "too many values to unpack (expected %d)", (int)expected);
+ #else
+ "too many values to unpack (expected %zd)", expected);
+ #endif
+}
+
+static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
+ PyObject *item;
+ if (!(item = PyIter_Next(iter))) {
+ if (!PyErr_Occurred()) {
+ __Pyx_RaiseNeedMoreValuesError(index);
+ }
+ }
+ return item;
+}
+
+static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
+ PyObject *item;
+ if ((item = PyIter_Next(iter))) {
+ Py_DECREF(item);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ }
+ else if (!PyErr_Occurred())
+ return 0;
+ else
+ return -1;
+}
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->exc_type;
+ *value = tstate->exc_value;
+ *tb = tstate->exc_traceback;
+ Py_XINCREF(*type);
+ Py_XINCREF(*value);
+ Py_XINCREF(*tb);
+}
+
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = type;
+ tstate->exc_value = value;
+ tstate->exc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
+ PyObject *py_import = 0;
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
+ if (!py_import)
+ goto bad;
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, NULL);
+bad:
+ Py_XDECREF(empty_list);
+ Py_XDECREF(py_import);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ 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;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
+bad:
+ return;
+}
+#endif
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
+ const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(uint32_t) == sizeof(char)) ||
+ (sizeof(uint32_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(uint32_t) == sizeof(int)) ||
+ (sizeof(uint32_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
+ little, !is_unsigned);
+ }
+}
+
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
+ const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint32_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint32_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint32_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint32_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint32_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ return (uint32_t)-1;
+ }
+}
+
+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;
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned char" :
+ "value too large to convert to unsigned char");
+ }
+ return (unsigned char)-1;
+ }
+ return (unsigned char)val;
+ }
+ return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+ const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned short" :
+ "value too large to convert to unsigned short");
+ }
+ return (unsigned short)-1;
+ }
+ return (unsigned short)val;
+ }
+ return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+ const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned int" :
+ "value too large to convert to unsigned int");
+ }
+ return (unsigned int)-1;
+ }
+ return (unsigned int)val;
+ }
+ return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+ const char neg_one = (char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to char" :
+ "value too large to convert to char");
+ }
+ return (char)-1;
+ }
+ return (char)val;
+ }
+ return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+ const short neg_one = (short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to short" :
+ "value too large to convert to short");
+ }
+ return (short)-1;
+ }
+ return (short)val;
+ }
+ return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+ const signed char neg_one = (signed char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed char" :
+ "value too large to convert to signed char");
+ }
+ return (signed char)-1;
+ }
+ return (signed char)val;
+ }
+ return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+ const signed short neg_one = (signed short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed short" :
+ "value too large to convert to signed short");
+ }
+ return (signed short)-1;
+ }
+ return (signed short)val;
+ }
+ return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+ const signed int neg_one = (signed int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed int" :
+ "value too large to convert to signed int");
+ }
+ return (signed int)-1;
+ }
+ return (signed int)val;
+ }
+ return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+ const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ unsigned long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned long)-1;
+ val = __Pyx_PyInt_AsUnsignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+ const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ unsigned PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+ const long neg_one = (long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long)-1;
+ val = __Pyx_PyInt_AsLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+ const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return (PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+ const signed long neg_one = (signed long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
+ }
+ return (signed long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ signed long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed long)-1;
+ val = __Pyx_PyInt_AsSignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+ const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ signed PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsSignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static void __Pyx_WriteUnraisable(const char *name) {
+ PyObject *old_exc, *old_val, *old_tb;
+ PyObject *ctx;
+ __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
+ #if PY_MAJOR_VERSION < 3
+ ctx = PyString_FromString(name);
+ #else
+ ctx = PyUnicode_FromString(name);
+ #endif
+ __Pyx_ErrRestore(old_exc, old_val, old_tb);
+ if (!ctx) {
+ PyErr_WriteUnraisable(Py_None);
+ } else {
+ PyErr_WriteUnraisable(ctx);
+ Py_DECREF(ctx);
+ }
+}
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+#ifndef __PYX_HAVE_RT_ImportType
+#define __PYX_HAVE_RT_ImportType
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
+ long size, int strict)
+{
+ PyObject *py_module = 0;
+ PyObject *result = 0;
+ PyObject *py_name = 0;
+ char warning[200];
+
+ py_module = __Pyx_ImportModule(module_name);
+ if (!py_module)
+ goto bad;
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(class_name);
+ #else
+ py_name = PyUnicode_FromString(class_name);
+ #endif
+ if (!py_name)
+ goto bad;
+ result = PyObject_GetAttr(py_module, py_name);
+ Py_DECREF(py_name);
+ py_name = 0;
+ Py_DECREF(py_module);
+ py_module = 0;
+ if (!result)
+ goto bad;
+ if (!PyType_Check(result)) {
+ PyErr_Format(PyExc_TypeError,
+ "%s.%s is not a type object",
+ module_name, class_name);
+ goto bad;
+ }
+ if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
+ PyOS_snprintf(warning, sizeof(warning),
+ "%s.%s size changed, may indicate binary incompatibility",
+ module_name, class_name);
+ #if PY_VERSION_HEX < 0x02050000
+ PyErr_Warn(NULL, warning);
+ #else
+ PyErr_WarnEx(NULL, warning, 0);
+ #endif
+ }
+ else if (((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%s.%s has the wrong size, try recompiling",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_module);
+ Py_XDECREF(result);
+ return 0;
+}
+#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;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ 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
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+
+static void __Pyx_AddTraceback(const char *funcname) {
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(__pyx_filename);
+ #else
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (__pyx_clineno) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_code = PyCode_New(
+ 0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*int kwonlyargcount,*/
+ #endif
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ __pyx_empty_bytes, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ __pyx_lineno, /*int firstlineno,*/
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ if (!py_code) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = __pyx_lineno;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ while (t->p) {
+ #if PY_MAJOR_VERSION < 3
+ if (t->is_unicode) {
+ *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+ } else if (t->intern) {
+ *t->p = PyString_InternFromString(t->s);
+ } else {
+ *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+ }
+ #else /* Python 3+ has unicode identifiers */
+ if (t->is_unicode | t->is_str) {
+ if (t->intern) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->encoding) {
+ *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
+ } else {
+ *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+ }
+ } else {
+ *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+ }
+ #endif
+ if (!*t->p)
+ return -1;
+ ++t;
+ }
+ return 0;
+}
+
+/* Type Conversion Functions */
+
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+ int is_true = x == Py_True;
+ if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
+ else return PyObject_IsTrue(x);
+}
+
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
+ PyNumberMethods *m;
+ const char *name = NULL;
+ PyObject *res = NULL;
+#if PY_VERSION_HEX < 0x03000000
+ if (PyInt_Check(x) || PyLong_Check(x))
+#else
+ if (PyLong_Check(x))
+#endif
+ return Py_INCREF(x), x;
+ m = Py_TYPE(x)->tp_as_number;
+#if PY_VERSION_HEX < 0x03000000
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Int(x);
+ }
+ else if (m && m->nb_long) {
+ name = "long";
+ res = PyNumber_Long(x);
+ }
+#else
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Long(x);
+ }
+#endif
+ if (res) {
+#if PY_VERSION_HEX < 0x03000000
+ if (!PyInt_Check(res) && !PyLong_Check(res)) {
+#else
+ if (!PyLong_Check(res)) {
+#endif
+ PyErr_Format(PyExc_TypeError,
+ "__%s__ returned non-%s (type %.200s)",
+ name, name, Py_TYPE(res)->tp_name);
+ Py_DECREF(res);
+ return NULL;
+ }
+ }
+ else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_TypeError,
+ "an integer is required");
+ }
+ return res;
+}
+
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
+ Py_ssize_t ival;
+ PyObject* x = PyNumber_Index(b);
+ if (!x) return -1;
+ ival = PyInt_AsSsize_t(x);
+ Py_DECREF(x);
+ return ival;
+}
+
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
+#if PY_VERSION_HEX < 0x02050000
+ if (ival <= LONG_MAX)
+ return PyInt_FromLong((long)ival);
+ else {
+ unsigned char *bytes = (unsigned char *) &ival;
+ int one = 1; int little = (int)*(unsigned char*)&one;
+ return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+ }
+#else
+ return PyInt_FromSize_t(ival);
+#endif
+}
+
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+ unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+ if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+ return (size_t)-1;
+ } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t)-1;
+ }
+ return (size_t)val;
+}
+
+
+#endif /* Py_PYTHON_H */
--- /dev/null
+cdef extern from "stdlib.h":
+ void free(void *)
+ void *malloc(size_t)
+ void *calloc(size_t,size_t)
+ void *realloc(void *,size_t)
+ int c_abs "abs" (int)
+ int c_abs "abs" (int)
+ int atoi( char *nptr)
+ long atol( char *nptr)
+ double atof( char *nptr)
+
+cdef extern from "Python.h":
+ ctypedef struct FILE
+ FILE* PyFile_AsFile(object)
+ char *fgets(char *str, int size, FILE *ifile)
+ int feof(FILE *stream)
+ size_t strlen(char *s)
+ size_t getline(char **lineptr, size_t *n, FILE *stream)
+ char *strstr(char *, char *)
+ char *strchr(char *string, int c)
+ int fileno(FILE *stream)
+
+cdef extern from "string.h":
+ int strcmp(char *s1, char *s2)
+ int strncmp(char *s1,char *s2,size_t len)
+ char *strcpy(char *dest,char *src)
+ char *strncpy(char *dest,char *src, size_t len)
+ char *strdup(char *)
+ char *strcat(char *,char *)
+ size_t strlen(char *s)
+ int memcmp( void * s1, void *s2, size_t len )
+ void *memcpy(void *dest, void *src, size_t n)
+ void *memchr(void *s, int c, size_t n)
+
+cdef extern from "stdint.h":
+ ctypedef int int64_t
+ ctypedef int int32_t
+ ctypedef int uint32_t
+ ctypedef int uint8_t
+ ctypedef int uint64_t
+
+cdef class TupleProxy:
+
+ cdef:
+ char * data
+ char ** fields
+ int nfields
+ int index
+ int nbytes
+ int offset
+ cdef bint is_modified
+
+ cdef int getMaxFields( self, size_t nbytes )
+
+ cdef take( self, char * buffer, size_t nbytes )
+ cdef present( self, char * buffer, size_t nbytes )
+ cdef copy( self, char * buffer, size_t nbytes )
+ cdef update( self, char * buffer, size_t nbytes )
+
+cdef class GTFProxy( TupleProxy) :
+
+ cdef:
+ char * contig
+ char * source
+ char * feature
+ uint32_t start
+ uint32_t end
+ char * score
+ char * strand
+ char * frame
+ char * attributes
+ cdef bint hasOwnAttributes
+
+ cdef int getMaxFields( self, size_t nbytes )
+ cdef update( self, char * buffer, size_t nbytes )
+
+cdef class NamedTupleProxy( TupleProxy) :
+ pass
+
+cdef class BedProxy( NamedTupleProxy) :
+
+ cdef:
+ char * contig
+ uint32_t start
+ uint32_t end
+ int bedfields
+
+ cdef int getMaxFields( self, size_t nbytes )
+ cdef update( self, char * buffer, size_t nbytes )
+
+cdef class VCFProxy( NamedTupleProxy) :
+
+ cdef:
+ char * contig
+ uint32_t pos
+
+ cdef update( self, char * buffer, size_t nbytes )
--- /dev/null
+import types
+from cpython cimport PyString_FromStringAndSize, PyString_AsString, PyString_AS_STRING
+
+cdef char * nextItem( char * buffer ):
+ cdef char * pos
+ pos = strchr( buffer, '\t' )
+ if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
+ pos[0] = '\0'
+ pos += 1
+ return pos
+
+cdef char *StrOrEmpty( char * buffer ):
+ if buffer == NULL: return ""
+ else: return buffer
+
+cdef int isNew( char * p, char * buffer, size_t nbytes ):
+ if p == NULL: return 0
+ return not (buffer <= p < buffer + nbytes )
+
+cdef class TupleProxy:
+ '''Proxy class for access to parsed row as a tuple.
+
+ This class represents a table row for fast read-access.
+
+ Access to individual fields is via the [] operator.
+
+ Only read-only access is implemented.
+ '''
+
+ def __cinit__(self ):
+ self.data = NULL
+ self.fields = NULL
+ self.index = 0
+ self.nbytes = 0
+ self.is_modified = 0
+ self.nfields = 0
+ # start counting at field offset
+ self.offset = 0
+
+ def __dealloc__(self):
+ cdef int x
+ if self.is_modified:
+ for x from 0 <= x < self.nfields:
+ if isNew( self.fields[x], self.data, self.nbytes ):
+ free( self.fields[x] )
+ self.fields[x] = NULL
+
+ if self.data != NULL: free(self.data)
+ if self.fields != NULL: free( self.fields )
+
+ cdef take( self, char * buffer, size_t nbytes ):
+ '''start presenting buffer.
+
+ Take ownership of the pointer.
+ '''
+ self.data = buffer
+ self.nbytes = nbytes
+ self.update( buffer, nbytes )
+
+ cdef present( self, char * buffer, size_t nbytes ):
+ '''start presenting buffer.
+
+ Do not take ownership of the pointer.
+ '''
+ self.update( buffer, nbytes )
+
+ cdef copy( self, char * buffer, size_t nbytes ):
+ '''start presenting buffer.
+
+ Take a copy of buffer.
+ '''
+ cdef int s
+ # +1 for '\0'
+ s = sizeof(char) * (nbytes + 1)
+ self.data = <char*>malloc( s )
+ if self.data == NULL:
+ raise ValueError("out of memory" )
+ self.nbytes = nbytes
+ memcpy( <char*>self.data, buffer, s )
+ self.update( self.data, nbytes )
+
+ cdef int getMaxFields( self, size_t nbytes ):
+ '''initialize fields.'''
+ return nbytes / 2
+
+ cdef update( self, char * buffer, size_t nbytes ):
+ '''update internal data.
+
+ Update starts work in buffer, thus can be used
+ to collect any number of fields until nbytes
+ is exhausted.
+
+ If max_fields is set, the number of fields is initialized to max_fields.
+
+ '''
+ cdef char * pos
+ cdef char * old_pos
+ cdef int field
+ cdef int max_fields, x
+
+ if buffer[nbytes] != 0:
+ raise ValueError( "incomplete line at %s" % buffer )
+
+ #################################
+ # clear data
+ if self.fields != NULL: free(self.fields)
+
+ for field from 0 <= field < self.nfields:
+ if isNew( self.fields[field], self.data, self.nbytes ):
+ free( self.fields[field] )
+
+ self.is_modified = self.nfields = 0
+
+ #################################
+ # allocate new
+ max_fields = self.getMaxFields( nbytes )
+ self.fields = <char **>calloc( max_fields, sizeof(char *) )
+ if self.fields == NULL:
+ raise ValueError("out of memory" )
+
+ #################################
+ # start filling
+ field = 0
+ self.fields[field] = pos = buffer
+ field += 1
+ old_pos = pos
+
+ while 1:
+
+ pos = <char*>memchr( pos, '\t', nbytes )
+ if pos == NULL: break
+ pos[0] = '\0'
+ pos += 1
+ self.fields[field] = pos
+ field += 1
+ if field >= max_fields:
+ raise ValueError("row too large - more than %i fields" % max_fields )
+ nbytes -= pos - old_pos
+ if nbytes < 0: break
+ old_pos = pos
+
+ self.nfields = field
+
+ def __getitem__( self, key ):
+
+ cdef int i = key
+ if i < 0: i += self.nfields
+ if i < 0: raise IndexError( "list index out of range" )
+ i += self.offset
+ if i >= self.nfields:
+ raise IndexError( "list index out of range" )
+ return self.fields[i]
+
+ def _setindex( self, index, value ):
+ '''set item at idx index.'''
+ cdef int idx = index
+ if idx < 0: raise IndexError( "list index out of range" )
+ if idx >= self.nfields:
+ raise IndexError( "list index out of range" )
+
+ if isNew( self.fields[idx], self.data, self.nbytes ):
+ free( self.fields[idx] )
+
+ self.is_modified = 1
+
+ if value == None:
+ self.fields[idx] = NULL
+ return
+
+ # conversion with error checking
+ cdef char * tmp = PyString_AsString( value )
+ self.fields[idx] = <char*>malloc( (strlen( tmp ) + 1) * sizeof(char) )
+ if self.fields[idx] == NULL:
+ raise ValueError("out of memory" )
+ strcpy( self.fields[idx], tmp )
+
+ def __setitem__(self, index, value ):
+ '''set item at *index* to *value*'''
+ cdef int i = index
+ if i < 0: i += self.nfields
+ i += self.offset
+
+ self._setindex( i, value )
+
+ def __len__(self):
+ return self.nfields
+
+ def __iter__(self):
+ self.index = 0
+ return self
+
+ def __next__(self):
+ """python version of next().
+ """
+ if self.index >= self.nfields:
+ raise StopIteration
+ cdef char * retval = self.fields[self.index]
+ self.index += 1
+ if retval == NULL: return None
+ else: return retval
+
+ def __str__(self):
+ '''return original data'''
+ # copy and replace \0 bytes with \t characters
+ if self.is_modified:
+ # todo: treat NULL values
+ return "\t".join( [StrOrEmpty( self.fields[x]) for x in xrange(0, self.nfields ) ] )
+ else:
+ cpy = <char*>calloc( sizeof(char), self.nbytes+1 )
+ if cpy == NULL:
+ raise ValueError("out of memory" )
+ memcpy( cpy, self.data, self.nbytes+1)
+ for x from 0 <= x < self.nbytes:
+ if cpy[x] == '\0': cpy[x] = '\t'
+ result = PyString_FromStringAndSize(cpy, self.nbytes)
+ free(cpy)
+ return result
+
+def toDot( v ):
+ '''convert value to '.' if None'''
+ if v == None: return "."
+ else: return str(v)
+
+def quote( v ):
+ '''return a quoted attribute.'''
+ if type(v) in types.StringTypes:
+ return '"%s"' % v
+ else:
+ return str(v)
+
+cdef class GTFProxy( TupleProxy ):
+ '''Proxy class for access to GTF fields.
+
+ This class represents a GTF entry for fast read-access.
+ Write-access has been added as well, though some care must
+ be taken. If any of the string fields (contig, source, ...)
+ are set, the new value is tied to the lifetime of the
+ argument that was supplied.
+
+ The only exception is the attributes field when set from
+ a dictionary - this field will manage its own memory.
+
+ '''
+
+ def __cinit__(self ):
+ # automatically calls TupleProxy.__cinit__
+ self.hasOwnAttributes = False
+
+ def __dealloc__(self):
+ # automatically calls TupleProxy.__dealloc__
+ if self.hasOwnAttributes:
+ free(self.attributes)
+
+ cdef int getMaxFields( self, size_t nbytes ):
+ '''return max number of fields.'''
+ return 9
+
+ cdef update( self, char * buffer, size_t nbytes ):
+ '''update internal data.
+
+ nbytes does not include the terminal '\0'.
+ '''
+ cdef int end
+ cdef char * cstart, * cend, * cscore
+ self.contig = buffer
+ cdef char * pos
+
+ if buffer[nbytes] != 0:
+ raise ValueError( "incomplete line at %s" % buffer )
+
+ self.source = pos = nextItem( buffer )
+ self.feature = pos = nextItem( pos )
+ cstart = pos = nextItem( pos )
+ cend = pos = nextItem( pos )
+ self.score = pos = nextItem( pos )
+ self.strand = pos = nextItem( pos )
+ self.frame = pos = nextItem( pos )
+ self.attributes = pos = nextItem( pos )
+
+ self.start = atoi( cstart ) - 1
+ self.end = atoi( cend )
+
+ property contig:
+ '''contig of feature.'''
+ def __get__( self ): return self.contig
+ def __set__( self, value ):
+ self.is_modified = True
+ self.contig = value
+
+ property feature:
+ '''feature name.'''
+ def __get__( self ): return self.feature
+ def __set__( self, value ):
+ self.is_modified = True
+ self.feature = value
+
+ property source:
+ '''feature source.'''
+ def __get__( self ): return self.source
+ def __set__( self, value ):
+ self.is_modified = True
+ self.source = value
+
+ property start:
+ '''feature start (in 0-based open/closed coordinates).'''
+ def __get__( self ): return self.start
+ def __set__( self, value ):
+ self.is_modified = True
+ self.start = value
+
+ property end:
+ '''feature end (in 0-based open/closed coordinates).'''
+ def __get__( self ): return self.end
+ def __set__( self, value ):
+ self.is_modified = True
+ self.end = value
+
+ property score:
+ '''feature score.'''
+ def __get__( self ):
+ if self.score[0] == '.' and self.score[1] == '\0' :
+ return None
+ else:
+ return atof(self.score)
+ def __set__( self, value ):
+ self.is_modified = True
+ self.score = value
+
+ property strand:
+ '''feature strand.'''
+ def __get__( self ): return self.strand
+ def __set__( self, value ):
+ self.is_modified = True
+ self.strand = value
+
+ property frame:
+ '''feature frame.'''
+ def __get__( self ): return self.frame
+ def __set__( self, value ):
+ self.is_modified = True
+ self.frame = value
+
+ property attributes:
+ '''feature attributes (as a string).'''
+ def __get__( self ): return self.attributes
+ def __set__( self, value ):
+ self.is_modified = True
+ self.attributes = value
+
+ def asDict( self ):
+ """parse attributes - return as dict
+ """
+
+ # remove comments
+ attributes = self.attributes
+
+ # separate into fields
+ fields = [ x.strip() for x in attributes.split(";")[:-1]]
+
+ result = {}
+
+ for f in fields:
+
+ d = [ x.strip() for x in f.split(" ")]
+
+ n,v = d[0], d[1]
+ if len(d) > 2: v = d[1:]
+
+ if v[0] == '"' and v[-1] == '"':
+ v = v[1:-1]
+ else:
+ ## try to convert to a value
+ try:
+ v = float( v )
+ v = int( v )
+ except ValueError:
+ pass
+ except TypeError:
+ pass
+
+ result[n] = v
+
+ return result
+
+ def fromDict( self, d ):
+ '''set attributes from a dictionary.'''
+ cdef char * p
+ cdef int l
+
+ # clean up if this field is set twice
+ if self.hasOwnAttributes:
+ free(self.attributes)
+
+ aa = []
+ for k,v in d.items():
+ if type(v) == types.StringType:
+ aa.append( '%s "%s"' % (k,v) )
+ else:
+ aa.append( '%s %s' % (k,str(v)) )
+
+ a = "; ".join( aa ) + ";"
+ p = a
+ l = len(a)
+ self.attributes = <char *>calloc( l + 1, sizeof(char) )
+ if self.attributes == NULL:
+ raise ValueError("out of memory" )
+ memcpy( self.attributes, p, l )
+
+ self.hasOwnAttributes = True
+ self.is_modified = True
+
+ def __str__(self):
+ cdef char * cpy
+ cdef int x
+
+ if self.is_modified:
+ return "\t".join(
+ (self.contig,
+ self.source,
+ self.feature,
+ str(self.start+1),
+ str(self.end),
+ toDot(self.score),
+ self.strand,
+ self.frame,
+ self.attributes ) )
+ else:
+ return TupleProxy.__str__(self)
+
+ def invert( self, int lcontig ):
+ '''invert coordinates to negative strand coordinates
+
+ This method will only act if the feature is on the
+ negative strand.'''
+
+ if self.strand[0] == '-':
+ start = min(self.start, self.end)
+ end = max(self.start, self.end)
+ self.start, self.end = lcontig - end, lcontig - start
+
+ def keys( self ):
+ '''return a list of attributes defined in this entry.'''
+ r = self.attributes
+ return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ]
+
+ def __getitem__(self, item):
+ return self.__getattr__( item )
+
+ def __getattr__(self, item ):
+ """Generic lookup of attribute from GFF/GTF attributes
+ Only called if there *isn't* an attribute with this name
+ """
+ cdef char * start
+ cdef char * query
+ cdef char * cpy
+ cdef char * end
+ cdef int l
+ query = item
+
+ start = strstr( self.attributes, query)
+ if start == NULL:
+ raise AttributeError("'GTFProxy' has no attribute '%s'" % item )
+
+ start += strlen(query) + 1
+ # skip gaps before
+ while start[0] == " ": start += 1
+ if start[0] == '"':
+ start += 1
+ end = start
+ while end[0] != '\0' and end[0] != '"': end += 1
+ l = end - start + 1
+ cpy = <char*>calloc( l, sizeof(char ) )
+ if cpy == NULL: raise ValueError("out of memory" )
+ memcpy( cpy, start, l )
+ cpy[l-1] = '\0'
+ result = cpy
+ free(cpy)
+ return result
+ else:
+ return start
+
+ def setAttribute( self, name, value ):
+ '''convenience method to set an attribute.'''
+ r = self.asDict()
+ r[name] = value
+ self.fromDict( r )
+
+cdef class NamedTupleProxy( TupleProxy ):
+
+ map_key2field = {}
+
+ def __setattr__(self, key, value ):
+ '''set attribute.'''
+ cdef int idx
+ idx, f = self.map_key2field[key]
+ if self.nfields < idx:
+ raise KeyError( "field %s not set" % key )
+ TupleProxy.__setitem__(self, idx, str(value) )
+
+ def __getattr__(self, key ):
+ cdef int idx
+ idx, f = self.map_key2field[key]
+ if self.nfields < idx:
+ raise KeyError( "field %s not set" % key )
+ return f( self.fields[idx] )
+
+cdef class BedProxy( NamedTupleProxy ):
+ '''Proxy class for access to Bed fields.
+
+ This class represents a GTF entry for fast read-access.
+ '''
+ map_key2field = {
+ 'contig' : (0, str),
+ 'start' : (1, int),
+ 'end' : (2, int),
+ 'name' : (3, str),
+ 'score' : (4, float),
+ 'strand' : (5, str),
+ 'thickStart' : (6,int ),
+ 'thickEnd' : (7,int),
+ 'itemRGB' : (8,str),
+ 'blockCount': (9,int),
+ 'blockSizes': (10,str),
+ 'blockStarts': (11,str), }
+
+ cdef int getMaxFields( self, size_t nbytes ):
+ '''return max number of fields.'''
+ return 12
+
+ cdef update( self, char * buffer, size_t nbytes ):
+ '''update internal data.
+
+ nbytes does not include the terminal '\0'.
+ '''
+ TupleProxy.update( self, buffer, nbytes )
+
+ if self.nfields < 3:
+ raise ValueError( "bed format requires at least three columns" )
+
+ # determines bed format
+ self.bedfields = self.nfields
+
+ # do automatic conversion
+ self.contig = self.fields[0]
+ self.start = atoi( self.fields[1] )
+ self.end = atoi( self.fields[2] )
+
+ # __setattr__ in base class seems to take precedence
+ # hence implement setters in __setattr__
+ #property start:
+ # def __get__( self ): return self.start
+ #property end:
+ # def __get__( self ): return self.end
+
+ def __str__(self):
+
+ cdef int save_fields = self.nfields
+ # ensure fields to use correct format
+ self.nfields = self.bedfields
+ retval = TupleProxy.__str__( self )
+ self.nfields = save_fields
+ return retval
+
+ def __setattr__(self, key, value ):
+ '''set attribute.'''
+ if key == "start": self.start = value
+ elif key == "end": self.end = value
+
+ cdef int idx
+ idx, f = self.map_key2field[key]
+ TupleProxy._setindex(self, idx, str(value) )
+
+cdef class VCFProxy( NamedTupleProxy ):
+ '''Proxy class for access to VCF fields.
+
+ The genotypes are accessed via index.
+ '''
+ map_key2field = {
+ 'contig' : (0, str),
+ 'pos' : (1, int),
+ 'id' : (2, str),
+ 'ref' : (3, str),
+ 'alt' : (4, str),
+ 'qual' : (5, str),
+ 'filter' : (6,str),
+ 'info' : (7,str),
+ 'format' : (8,str) }
+
+ def __cinit__(self ):
+ # automatically calls TupleProxy.__cinit__
+ # start indexed access at genotypes
+ self.offset = 9
+
+ cdef update( self, char * buffer, size_t nbytes ):
+ '''update internal data.
+
+ nbytes does not include the terminal '\0'.
+ '''
+ TupleProxy.update( self, buffer, nbytes )
+
+ self.contig = self.fields[0]
+ # vcf counts from 1 - correct here
+ self.pos = atoi( self.fields[1] ) - 1
+
+ def __len__(self):
+ return max(0, self.nfields - 9)
+
+ def __setattr__(self, key, value ):
+ '''set attribute.'''
+ if key == "pos":
+ self.pos = value
+ value += 1
+
+ cdef int idx
+ idx, f = self.map_key2field[key]
+ TupleProxy._setindex(self, idx, str(value) )
+
--- /dev/null
+#
+# Code to read, write and edit VCF files
+#
+# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
+# 'chrom': string
+# 'pos': integer
+# 'id': string
+# 'ref': string
+# 'alt': list of strings
+# 'qual': integer
+# 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
+# 'info': dictionary of values (see below)
+# 'format': list of keys (strings)
+# sample keys: dictionary of values (see below)
+#
+# The sample keys are accessible through vcf.getsamples()
+#
+# A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map
+# to a list, containign integers, floats, strings, or characters. Missing values are replaced
+# by a particular value, often -1 or .
+#
+# Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples),
+# the first (and last) the integer representing an allele, and the second the separation character.
+# Note that there is just one genotype per sample, but for consistency the single element is stored in a list.
+#
+# Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible
+# through getheader()
+#
+# The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding
+# 0-based half-open segments. Only variants with a position inside the segment will be parsed. A regions
+# parser is available under parse_regions.
+#
+# When instantiated, a reference can be passed to the VCF class. This may be any class that supports a
+# fetch(chrom, start, end) method.
+#
+#
+#
+# NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file.
+#
+#
+#
+# TODO:
+# only v4.0 writing is complete; alleles are not converted to v3.3 format
+#
+
+from collections import namedtuple, defaultdict
+from operator import itemgetter
+import sys, re, copy, bisect
+
+import pysam
+
+gtsRegEx = re.compile("[|/\\\\]")
+alleleRegEx = re.compile('^[ACGTN]+$')
+
+# Utility function. Uses 0-based coordinates
+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()
+ sequence = fa.fetch(chrom, start, end).upper()
+ if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
+ return sequence
+
+# Utility function. Parses a region string
+def parse_regions( string ):
+ result = []
+ for r in string.split(','):
+ elts = r.split(':')
+ chrom, start, end = elts[0], 0, 3000000000
+ if len(elts)==1: pass
+ elif len(elts)==2:
+ if len(elts[1])>0:
+ 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])
+ except: raise ValueError("Don't understand region string '%s'" % r)
+ else:
+ raise ValueError("Don't understand region string '%s'" % r)
+ result.append( (chrom,start,end) )
+ return result
+
+
+FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
+
+###########################################################################################################
+#
+# New class
+#
+###########################################################################################################
+
+class VCFRecord:
+ '''vcf record.
+
+ initialized from data and vcf meta
+ '''
+
+ data = None
+ vcf = None
+
+ def __init__(self, data, vcf):
+ self.data, self.vcf = data, vcf
+
+ if len(data) != len(self.vcf._samples):
+ self.error(str(data),
+ self.BAD_NUMBER_OF_COLUMNS,
+ "expected %s for %s samples (%s), got %s" % \
+ (len(self.vcf._samples),
+ len(self.vcf._samples),
+ self.vcf._samples,
+ len(data)))
+
+ property contig:
+ def contig( self ): return self.data[0]
+
+ property pos:
+ def __get__( self ):
+ return self.data.pos
+
+ property id:
+ def __get__( self ): return self.data[2]
+
+ property ref:
+ def __get__(self ):
+ # note: gerton substitutes reference if it can be fixed.
+ return self.data[3].upper()
+
+ property alt:
+ def __get__(self):
+ # convert v3.3 to v4.0 alleles below
+ alt = self.data[4]
+ if alt == ".": alt = []
+ else: alt = alt.upper().split(',')
+ return alt
+
+ property qual:
+ def __get__(self):
+ qual = self.data[5]
+ if qual == ".": qual = -1
+ else:
+ try: qual = float(qual)
+ except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+ property filter:
+ def __get__(self):
+ # 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(';')
+
+ return filter
+
+ property info:
+ def __get__(self):
+ col = self.data[7]
+ # dictionary of keys, and list of values
+ info = {}
+ if col != ".":
+ for blurp in col.split(';'):
+ elts = blurp.split('=')
+ if len(elts) == 1: v = None
+ elif len(elts) == 2: v = elts[1]
+ else: self.error(str(self.data),self.ERROR_INFO_STRING)
+ info[elts[0]] = self.parse_formatdata(elts[0], v, self.vcf._info, line)
+ return info
+
+ property format:
+ def __get__(self):
+ return self.data[8].split(':')
+
+ def __getitem__(self, key):
+
+ # parse sample columns
+ values = self.data[self.vcf._sample2column[key]].split(':')
+ alt = self.alt
+ format = self.format
+
+ 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)))
+
+ result = {}
+ for idx in range(len(format)):
+ expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
+ if idx < len(values): value = values[idx]
+ else:
+ if expected == -1: value = "."
+ else: value = ",".join(["."]*expected)
+
+ result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, line)
+ 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]]))
+ 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]
+
+ return result
+
+ def __str__(self):
+ return str(self.data)
+
+class VCF:
+
+ # types
+ NT_UNKNOWN = 0
+ NT_NUMBER = 1
+ NT_ALLELES = 2
+ NT_NR_ALLELES = 3
+ NT_GENOTYPES = 4
+ NT_PHASED_GENOTYPES = 5
+
+ _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
+ 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
+ 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
+ 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
+ 4:"POS_NOT_NUMERICAL:Position column is not numerical",
+ 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
+ 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
+ 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
+ 8:"POS_NOT_POSITIVE:Position field must be >0",
+ 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
+ 10:"ERROR_INFO_STRING:Error while parsing info field",
+ 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
+ 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
+ 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
+ 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
+ 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
+ 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
+ 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
+ 18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
+ 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
+ 20:"MISSING_REF:Reference allele missing",
+ 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
+ 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
+ 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
+ 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
+ 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
+ 26:"WRONG_REF:Wrong reference %s",
+ 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
+ 28:"BAD_CHR_TAG:Error calculating chr tag for %s",
+ 29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
+ 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"
+ }
+
+ # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
+ _header = []
+
+ # version number; 33=v3.3; 40=v4.0
+ _version = 40
+
+ # info, filter and format data
+ _info = {}
+ _filter = {}
+ _format = {}
+
+ # header; and required columns
+ _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
+ _samples = []
+
+ # control behaviour
+ _ignored_errors = set([11]) # ERROR_UNKNOWN_KEY
+ _warn_errors = set([])
+ _leftalign = False
+
+ # reference sequence
+ _reference = None
+
+ # regions to include; None includes everything
+ _regions = None
+
+ # statefull stuff
+ _lineno = -1
+ _line = None
+ _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
+ if _copy != None:
+ self._leftalign = _copy._leftalign
+ self._header = _copy._header[:]
+ self._version = _copy._version
+ self._info = copy.deepcopy(_copy._info)
+ self._filter = copy.deepcopy(_copy._filter)
+ self._format = copy.deepcopy(_copy._format)
+ self._samples = _copy._samples[:]
+ self._sample2column = copy.deepcopy(_copy._sample2column)
+ self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
+ self._warn_errors = copy.deepcopy(_copy._warn_errors)
+ self._reference = _copy._reference
+ self._regions = _copy._regions
+ if reference: self._reference = reference
+ if regions: self._regions = regions
+ if leftalign: self._leftalign = leftalign
+ self._lines = lines
+
+ def error(self,line,error,opt=None):
+ if error in self._ignored_errors: return
+ errorlabel, errorstring = self._errors[error].split(':')
+ if opt: errorstring = errorstring % opt
+ errwarn = ["Error","Warning"][error in self._warn_errors]
+ sys.stderr.write("Line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring))
+ if error in self._warn_errors: return
+ raise ValueError(errorstring)
+
+ def parse_format(self,line,format,filter=False):
+ if self._version == 40:
+ if not format.startswith('<'):
+ self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+ format = "<"+format
+ if not format.endswith('>'):
+ self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+ format += ">"
+ format = format[1:-1]
+ data = {'id':None,'number':None,'type':None,'descr':None}
+ idx = 0
+ while len(format.strip())>0:
+ elts = format.strip().split(',')
+ 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)
+ 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]
+ elif first.startswith('Number='): data['number'] = first.split('=')[1]
+ elif first.startswith('Type='): data['type'] = first.split('=')[1]
+ elif first.startswith('Description='):
+ elts = format.split('"')
+ if len(elts)<3:
+ self.error(line,self.FORMAT_MISSING_QUOTES)
+ elts = first.split('=') + [rest]
+ data['descr'] = elts[1]
+ rest = '"'.join(elts[2:])
+ if rest.startswith(','): rest = rest[1:]
+ else:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ format = rest
+ 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)
+ if not data['descr']:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ data['descr'] = '<none>'
+ if not data['type'] and not data['number']:
+ # fine, ##filter format
+ 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)
+ # 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'] = '.'
+ if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ try:
+ n = int(data['number'])
+ t = self.NT_NUMBER
+ except ValueError:
+ 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
+ elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
+ else:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ 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:
+ 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"
+ 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"
+ else:
+ raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
+ values.append( ('Number',nmb) )
+ values.append( ('Type', fmt.type) )
+ values.append( ('Description', '"' + fmt.description + '"') )
+ if self._version == 33:
+ format = ",".join(v for k,v in values)
+ else:
+ format = "<" + (",".join( "%s=%s" % (k,v) for (k,v) in values )) + ">"
+ return format
+
+ def get_expected(self, format, formatdict, alt):
+ fmt = formatdict[format]
+ 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
+ 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)
+ return 0
+
+
+ def _add_definition(self, formatdict, key, data, line ):
+ 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
+ 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)
+ return
+ if type(data[0]) == type(0):
+ formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
+ return
+ formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
+
+
+ # 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
+ d = {}
+ for k in data: d[k] = []
+ data = d
+ # convert missing values; and silently add definitions if required
+ for k in data:
+ self._add_definition( format, k, data[k], "(output)" )
+ for idx,v in enumerate(data[k]):
+ 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:
+ 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:
+ 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)
+ elif value:
+ if v != None: output.append( ','.join(map(str,v)) )
+ else: output.append( "." ) # should not happen
+ # snip off trailing missing data
+ while len(output) > 1:
+ last = output[-1].replace(',','').replace('.','')
+ if len(last)>0: break
+ output = output[:-1]
+ return separator.join(output)
+
+
+ def enter_default_format(self):
+ for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
+ FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
+ FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
+ FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
+ FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.')]:
+ if f.id not in self._format:
+ self._format[f.id] = f
+
+ def parse_header( self, line ):
+ assert line.startswith('##')
+ elts = line[2:].split('=')
+ key = elts[0].strip()
+ value = '='.join(elts[1:]).strip()
+ if key == "fileformat":
+ if value == "VCFv3.3":
+ self._version = 33
+ elif value == "VCFv4.0":
+ self._version = 40
+ elif value == "VCFv4.1":
+ # AH - for testing
+ self._version = 40
+ else:
+ self.error(line,self.UNKNOWN_FORMAT_STRING)
+ elif key == "INFO":
+ 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
+ elif key == "FORMAT":
+ f = self.parse_format(line, value)
+ self._format[ f.id ] = f
+ else:
+ # keep other keys in the header field
+ self._header.append( (key,value) )
+
+
+ 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))
+ 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"))))
+
+
+ def parse_heading( self, line ):
+ assert line.startswith('#')
+ assert not line.startswith('##')
+ headings = line[1:].split('\t')
+ if len(headings)==1 and len(line[1:].split()) >= 9:
+ self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
+ headings = line[1:].split()
+
+ for i,s in enumerate(self._required):
+
+ if len(headings)<=i or headings[i] != s:
+
+ if len(headings) <= i:
+ err = "(%sth entry not found)" % (i+1)
+ else:
+ err = "(found %s, expected %s)" % (headings[i],s)
+
+ #self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+ # allow FORMAT column to be absent
+ if len(headings) == 8:
+ headings.append("FORMAT")
+ else:
+ self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+ self._samples = headings[9:]
+ self._sample2column = dict( [(y,x) for x,y in enumerate( self._samples ) ] )
+
+ def write_heading( self, stream ):
+ stream.write("#" + "\t".join(self._required + self._samples) + "\n")
+
+ def convertGT(self, GTstring):
+ if GTstring == ".": return ["."]
+ try:
+ gts = gtsRegEx.split(GTstring)
+ 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:
+ self.error(self._line,self.BAD_GENOTYPE,GTstring)
+ return [".","|","."]
+
+
+ def convertGTback(self, GTdata):
+ 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)
+ if f == None:
+ self._add_definition(formatdict, key, value, line )
+ f = formatdict[key]
+ if f.type == "Flag":
+ 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:
+ 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):
+ try:
+ if v == ".": values[idx] = f.missingvalue
+ else: values[idx] = int(v)
+ except:
+ self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+ return [0] * len(values)
+ return values
+ elif f.type == "String":
+ self._line = line
+ if f.id == "GT": values = 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)
+ return values
+ elif f.type == "Float":
+ for idx,v in enumerate(values):
+ if v == ".": values[idx] = f.missingvalue
+ try: return map(float,values)
+ except:
+ self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+ return [0.0] * len(values)
+ else:
+ # can't happen
+ self.error(line,self.ERROR_INFO_STRING)
+
+
+ def inregion(self, chrom, pos):
+ if not self._regions: return True
+ for r in self._regions:
+ if r[0] == chrom and r[1] <= pos < r[2]: return True
+ return False
+
+
+ def parse_data( self, line, lineparse=False ):
+ cols = line.split('\t')
+ if len(cols) != len(self._samples)+9:
+ # gracefully deal with absent FORMAT column
+ if len(cols) == 8 and len(self._samples)==0:
+ cols.append("")
+ else:
+ 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)))
+
+ chrom = cols[0]
+
+ # get 0-based position
+ try: pos = int(cols[1])-1
+ except: self.error(line,self.POS_NOT_NUMERICAL)
+ if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
+
+ # implement filtering
+ if not self.inregion(chrom,pos): return None
+
+ # end of first-pass parse for sortedVCF
+ if lineparse: return chrom, pos, line
+
+ id = cols[2]
+
+ 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)
+ else: ref = ""
+ 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)
+
+ # make sure reference is sane
+ 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))
+ ref = faref
+
+ # convert v3.3 to v4.0 alleles below
+ if cols[4] == ".": alt = []
+ else: alt = cols[4].upper().split(',')
+
+ if cols[5] == ".": qual = -1
+ else:
+ try: qual = float(cols[5])
+ except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+ # 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(';')
+
+ # dictionary of keys, and list of values
+ info = {}
+ 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]
+ else: self.error(line,self.ERROR_INFO_STRING)
+ info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line)
+
+ # Gracefully deal with absent FORMAT column
+ if cols[8] == "": format = []
+ else: format = cols[8].split(':')
+
+ # 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
+ for f in format:
+ if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
+
+ # convert v3.3 alleles
+ if self._version == 33:
+ if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+ newalts = []
+ have_deletions = False
+ 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<seq> and D<num>
+ 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)
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ 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)
+ 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
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ a = ref[len(s):] # new deletion, deleting from pos
+ else:
+ self.error(line,self.V33_BAD_ALLELE)
+ newalts.append(a)
+ alt = newalts
+ # 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)
+ ref += addn
+ 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]
+ pos -= 1
+ else:
+ # format v4.0 -- just check for nucleotides
+ for allele in alt:
+ if not alleleRegEx.match(allele):
+ self.error(line,self.V40_BAD_ALLELE,allele)
+
+ # check for leading nucleotide in indel calls
+ for allele in alt:
+ 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)
+
+ # trim trailing bases in alleles
+ 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]
+
+ # left-align alleles, if a reference is available
+ if self._leftalign and self._reference:
+ while left < pos:
+ movable = True
+ for allele in alt:
+ if len(allele) > len(ref):
+ longest, shortest = allele, ref
+ else:
+ longest, shortest = ref, allele
+ 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:
+ 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
+ alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+ pos -= 1
+
+ # parse sample columns
+ samples = []
+ 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)))
+ for idx in range(len(format)):
+ expected = self.get_expected(format[idx], self._format, alt)
+ if idx < len(values): value = values[idx]
+ else:
+ if expected == -1: value = "."
+ else: value = ",".join(["."]*expected)
+ dict[format[idx]] = self.parse_formatdata(format[idx], value, 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]]))
+ 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 )
+
+ # done
+ d = {'chrom':chrom,
+ 'pos':pos, # return 0-based position
+ 'id':id,
+ 'ref':ref,
+ 'alt':alt,
+ 'qual':qual,
+ 'filter':filter,
+ 'info':info,
+ 'format':format}
+ for key,value in zip(self._samples,samples):
+ d[key] = value
+
+ return d
+
+
+ def write_data(self, stream, data):
+ 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'])
+ if data['filter'] == None: filter = "."
+ elif data['filter'] == []:
+ if self._version == 33: filter = "0"
+ else: filter = "PASS"
+ else: filter = ';'.join(data['filter'])
+ if data['qual'] == -1: qual = "."
+ else: qual = str(data['qual'])
+
+ output = [data['chrom'],
+ str(data['pos']+1), # change to 1-based position
+ data['id'],
+ data['ref'],
+ alt,
+ qual,
+ filter,
+ self.format_formatdata( data['info'], self._info, separator=";" ),
+ self.format_formatdata( data['format'], self._format, value=False ) ]
+
+ for s in self._samples:
+ output.append( self.format_formatdata( data[s], self._format, key=False ) )
+
+ stream.write( "\t".join(output) + "\n" )
+
+ def _parse_header(self, stream):
+ self._lineno = 0
+ for line in stream:
+ self._lineno += 1
+ if line.startswith('##'):
+ self.parse_header( line.strip() )
+ elif line.startswith('#'):
+ self.parse_heading( line.strip() )
+ self.enter_default_format()
+ else:
+ break
+ return line
+
+ def _parse(self, line, stream):
+ if len(line.strip()) > 0:
+ d = self.parse_data( line.strip() )
+ if d: yield d
+ for line in stream:
+ self._lineno += 1
+ if self._lines and self._lineno > self._lines: raise StopIteration
+ d = self.parse_data( line.strip() )
+ if d: yield d
+
+ ######################################################################################################
+ #
+ # API follows
+ #
+ ######################################################################################################
+
+ def getsamples(self):
+ """ List of samples in VCF file """
+ return self._samples
+
+ def setsamples(self,samples):
+ """ List of samples in VCF file """
+ self._samples = samples
+
+ def getheader(self):
+ """ List of header key-value pairs (strings) """
+ return self._header
+
+ def setheader(self,header):
+ """ List of header key-value pairs (strings) """
+ self._header = header
+
+ def getinfo(self):
+ """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+ return self._info
+
+ def setinfo(self,info):
+ """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+ self._info = info
+
+ def getformat(self):
+ """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+ return self._format
+
+ def setformat(self,format):
+ """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+ self._format = format
+
+ def getfilter(self):
+ """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+ return self._filter
+
+ def setfilter(self,filter):
+ """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+ 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
+
+ def setregions(self, regions):
+ 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
+
+ def ignoreerror(self, errorstring):
+ try: self._ignored_errors.add(self.__dict__[errorstring])
+ 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)
+
+ def parse(self, stream):
+ """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
+ last_line = self._parse_header(stream)
+ # 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)
+
+ def write(self, stream, datagenerator):
+ """ Writes a VCF file to a stream, using a data generator (or list) """
+ self.write_header(stream)
+ self.write_heading(stream)
+ for data in datagenerator: self.write_data(stream,data)
+
+ def writeheader(self, stream):
+ """ Writes a VCF header """
+ self.write_header(stream)
+ 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
+ # 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
+ while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
+ ref1 = ref1[:-1]
+ alt1 = alt1[:-1]
+ while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
+ ref2 = ref2[:-1]
+ alt2 = alt2[:-1]
+ # now, the alternative alleles must be identical
+ return alt1 == alt2
+
+###########################################################################################################
+###########################################################################################################
+## API functions added by Andreas
+###########################################################################################################
+
+ def connect( self, filename ):
+ '''connect to tabix file.'''
+ self.tabixfile = pysam.Tabixfile( filename )
+ self._parse_header(self.tabixfile.header)
+
+ def fetch(self,
+ reference = None,
+ start = None,
+ end = None,
+ region = None ):
+ """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
+
+ iter = self.tabixfile.fetch( reference, start, end, region, parser = pysam.asVCF() )
+ for x in iter:
+ yield VCFRecord( x, self )
+
+ def validate( self, record ):
+ '''validate vcf record.
+
+ returns a validated record.
+ '''
+
+ chrom, pos = record.chrom, record.pos
+
+ # check reference
+ ref = record.ref
+ if ref == ".":
+ self.error(str(record),self.MISSING_REF)
+ if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+ else: ref = ""
+ else:
+ for c in ref:
+ if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF)
+ if "N" in ref: ref = get_sequence(chrom,
+ pos,
+ pos+len(ref),
+ self._reference)
+
+ # make sure reference is sane
+ if self._reference:
+ left = max(0,self.pos-100)
+ faref_leftflank = get_sequence(chrom,left,self.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
+
+ # check: format fields are defined
+ for f in record.format:
+ if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f)
+
+ # check: all filters are defined
+ for f in record.filter:
+ if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f)
+
+ # convert v3.3 alleles
+ if self._version == 33:
+ if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+ newalts = []
+ have_deletions = False
+ 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<seq> and D<num>
+ 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)
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ 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)
+ 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
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ a = ref[len(s):] # new deletion, deleting from pos
+ else:
+ self.error(line,self.V33_BAD_ALLELE)
+ newalts.append(a)
+ alt = newalts
+ # 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)
+ ref += addn
+ 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]
+ pos -= 1
+ else:
+ # format v4.0 -- just check for nucleotides
+ for allele in alt:
+ if not alleleRegEx.match(allele):
+ self.error(line,self.V40_BAD_ALLELE,allele)
+
+
+ # check for leading nucleotide in indel calls
+ for allele in alt:
+ 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)
+
+ # trim trailing bases in alleles
+ 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]
+
+ # left-align alleles, if a reference is available
+ if self._leftalign and self._reference:
+ while left < pos:
+ movable = True
+ for allele in alt:
+ if len(allele) > len(ref):
+ longest, shortest = allele, ref
+ else:
+ longest, shortest = ref, allele
+ 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:
+ 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
+ alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+ pos -= 1
+
+
+
+
from ctabix import *
import csamtools
import ctabix
+from cvcf import *
+import cvcf
import Pileup
import sys
import os
globals()[key] = SamtoolsDispatcher(cmd, parser)
# hack to export all the symbols from csamtools
-__all__ = csamtools.__all__ + \
+__all__ = \
+ csamtools.__all__ + \
ctabix.__all__ + \
+ cvcf.__all__ +\
[ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
- ["Pileup",]
+ ["Pileup" ]
from version import __version__, __samtools_version__
-/* Generated by Cython 0.13 on Fri Feb 11 09:01:21 2011 */
+/* Generated by Cython 0.13 on Tue Jun 7 17:24:36 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
/* Type declarations */
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":366
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":388
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
uint32_t flag;
} __pyx_t_9csamtools_MateData;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1332
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1478
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
int seq_len;
} __pyx_t_9csamtools___iterdata;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1510
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1655
* bam_plp_set_mask( self.pileup_iter, self.mask )
*
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
int reopen;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":80
- * return dest
- *
- * cdef class PileupRead # <<<<<<<<<<<<<<
- * cdef makePileupRead( bam_pileup1_t * src ):
- * '''fill a PileupRead object from a bam_pileup1_t * object.'''
- */
-
-struct __pyx_obj_9csamtools_PileupRead {
- PyObject_HEAD
- struct __pyx_obj_9csamtools_AlignedRead *_alignment;
- int32_t _qpos;
- int _indel;
- int _level;
- uint32_t _is_del;
- uint32_t _is_head;
- uint32_t _is_tail;
-};
-
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1125
- * ##-------------------------------------------------------------------
- * ##-------------------------------------------------------------------
- * cdef class IteratorRow: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over mapped reads.
- *
- */
-
-struct __pyx_obj_9csamtools_IteratorRow {
- PyObject_HEAD
-};
-
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1283
- *
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3192
+ * bam_maqindel_ret_destroy(self._r)
*
- * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
- * """iterates over all mapped reads by chaining iterators over each reference
- * """
- */
-
-struct __pyx_obj_9csamtools_IteratorRowAllRefs {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_obj_9csamtools_Samfile *samfile;
- int tid;
- struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
-};
-
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":71
- * return dest
+ * cdef class IndelCallerBase: # <<<<<<<<<<<<<<
+ * '''Base class for SNP callers.
*
- * cdef class PileupProxy # <<<<<<<<<<<<<<
- * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
- * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
*/
-struct __pyx_obj_9csamtools_PileupProxy {
+struct __pyx_obj_9csamtools_IndelCallerBase {
PyObject_HEAD
- bam_pileup1_t *plp;
- int tid;
- int pos;
- int n_pu;
+ bam_maqindel_opt_t *options;
+ struct __pyx_obj_9csamtools_IteratorColumn *iter;
+ int cap_mapQ;
+ int max_depth;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1144
- * pass
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3330
+ * return self._call()
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
+ * cdef class IteratorIndelCalls( IndelCallerBase ): # <<<<<<<<<<<<<<
+ * """*(IteratorColumn iterator)*
*
*/
-struct __pyx_obj_9csamtools_IteratorRowRegion {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
- bam1_t *b;
- int retval;
- struct __pyx_obj_9csamtools_Samfile *samfile;
- samfile_t *fp;
+struct __pyx_obj_9csamtools_IteratorIndelCalls {
+ struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":222
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244
* ## Public methods
* ######################################################################
* cdef class Fastafile: # <<<<<<<<<<<<<<
faidx_t *fastafile;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2892
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3103
* return call
*
* cdef class IndelCall: # <<<<<<<<<<<<<<
bam_maqindel_ret_t *_r;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2981
- * bam_maqindel_ret_destroy(self._r)
- *
- * cdef class IndelCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
+/* "pysam/csamtools.pxd":388
+ * cdef bam1_t * _delegate
*
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to samfile
*/
-struct __pyx_obj_9csamtools_IndelCallerBase {
+struct __pyx_obj_9csamtools_Samfile {
PyObject_HEAD
- bam_maqindel_opt_t *options;
- struct __pyx_obj_9csamtools_IteratorColumn *iter;
- int cap_mapQ;
- int max_depth;
+ struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
+ char *_filename;
+ samfile_t *samfile;
+ bam_index_t *index;
+ int isbam;
+ int isremote;
+ bam1_t *b;
+ char *mode;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":3119
- * return self._call()
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3287
+ * return call
*
- * cdef class IteratorIndelCalls( IndelCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
+ * cdef class IndelCaller( IndelCallerBase ): # <<<<<<<<<<<<<<
+ * '''*(IteratorColumn iterator_column )*
*
*/
-struct __pyx_obj_9csamtools_IteratorIndelCalls {
+struct __pyx_obj_9csamtools_IndelCaller {
struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2662
- *
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":91
+ * return dest
*
- * cdef class SNPCallerBase: # <<<<<<<<<<<<<<
- * '''Base class for SNP callers.
+ * cdef class PileupRead # <<<<<<<<<<<<<<
+ * cdef makePileupRead( bam_pileup1_t * src ):
+ * '''fill a PileupRead object from a bam_pileup1_t * object.'''
+ */
+
+struct __pyx_obj_9csamtools_PileupRead {
+ PyObject_HEAD
+ struct __pyx_obj_9csamtools_AlignedRead *_alignment;
+ int32_t _qpos;
+ int _indel;
+ int _level;
+ uint32_t _is_del;
+ uint32_t _is_head;
+ uint32_t _is_tail;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2816
+ * return retval, out_stderr, out_stdout
*
+ * cdef class SNPCall: # <<<<<<<<<<<<<<
+ * '''the results of a SNP call.'''
+ * cdef int _tid
*/
-struct __pyx_obj_9csamtools_SNPCallerBase {
+struct __pyx_obj_9csamtools_SNPCall {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtab;
- bam_maqcns_t *c;
- struct __pyx_obj_9csamtools_IteratorColumn *iter;
+ int _tid;
+ int _pos;
+ char _reference_base;
+ char _genotype;
+ int _consensus_quality;
+ int _snp_quality;
+ int _rms_mapping_quality;
+ int _coverage;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2735
- * sys.stdout.flush()
+/* "pysam/csamtools.pxd":383
*
- * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<<
- * """*(IteratorColumn iterator)*
+ * # need to declare all C fields and methods here
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
*
+ * # object that this AlignedRead represents
*/
-struct __pyx_obj_9csamtools_IteratorSNPCalls {
- struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
+struct __pyx_obj_9csamtools_AlignedRead {
+ PyObject_HEAD
+ bam1_t *_delegate;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1397
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542
* return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
PyObject *stepper;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1567
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712
* self.iterdata.seq = NULL
*
* cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2810
- * return call
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1187
+ * ##-------------------------------------------------------------------
+ * ##-------------------------------------------------------------------
+ * cdef class IteratorRow: # <<<<<<<<<<<<<<
+ * '''abstract base class for iterators over mapped reads.
*
- * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
+ */
+
+struct __pyx_obj_9csamtools_IteratorRow {
+ PyObject_HEAD
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1356
+ * if self.owns_samfile: samclose( self.fp )
*
+ * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
+ * """iterates over all mapped reads by chaining iterators over each reference
+ * """
*/
-struct __pyx_obj_9csamtools_SNPCaller {
- struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ int tid;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206
+ * pass
+ *
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
+ *
+ */
+
+struct __pyx_obj_9csamtools_IteratorRowRegion {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
+ bam_iter_t iter;
+ bam1_t *b;
+ int retval;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ samfile_t *fp;
+ int owns_samfile;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1596
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":3076
- * return call
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402
+ * raise StopIteration
*
- * cdef class IndelCaller( IndelCallerBase ): # <<<<<<<<<<<<<<
- * '''*(IteratorColumn iterator_column )*
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile)*
*
*/
-struct __pyx_obj_9csamtools_IndelCaller {
- struct __pyx_obj_9csamtools_IndelCallerBase __pyx_base;
+struct __pyx_obj_9csamtools_IteratorRowSelection {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtab;
+ bam1_t *b;
+ int current_pos;
+ samfile_t *fp;
+ PyObject *positions;
+ int owns_samfile;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":393
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873
*
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode='r', template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
+ * cdef class SNPCallerBase: # <<<<<<<<<<<<<<
+ * '''Base class for SNP callers.
*
*/
-struct __pyx_obj_9csamtools_Samfile {
+struct __pyx_obj_9csamtools_SNPCallerBase {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
- char *_filename;
- samfile_t *samfile;
- bam_index_t *index;
- int isbam;
- int isremote;
- bam1_t *b;
- char *mode;
+ struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtab;
+ bam_maqcns_t *c;
+ struct __pyx_obj_9csamtools_IteratorColumn *iter;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2605
- * return retval, out_stderr, out_stdout
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021
+ * return call
+ *
+ * cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<<
+ * '''*(IteratorColumn iterator_column )*
*
- * cdef class SNPCall: # <<<<<<<<<<<<<<
- * '''the results of a SNP call.'''
- * cdef int _tid
*/
-struct __pyx_obj_9csamtools_SNPCall {
- PyObject_HEAD
- int _tid;
- int _pos;
- char _reference_base;
- char _genotype;
- int _consensus_quality;
- int _snp_quality;
- int _rms_mapping_quality;
- int _coverage;
+struct __pyx_obj_9csamtools_SNPCaller {
+ struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946
+ * sys.stdout.flush()
+ *
+ * cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<<
+ * """*(IteratorColumn iterator)*
+ *
+ */
+
+struct __pyx_obj_9csamtools_IteratorSNPCalls {
+ struct __pyx_obj_9csamtools_SNPCallerBase __pyx_base;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1224
- * samclose( self.fp )
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292
+ * if self.owns_samfile: samclose( self.fp )
*
* cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
* """*(Samfile samfile, int reopen = True)*
struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
bam1_t *b;
samfile_t *fp;
+ int owns_samfile;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":64
- * ## private factory methods
- * #####################################################################
- * cdef class AlignedRead # <<<<<<<<<<<<<<
- * cdef makeAlignedRead(bam1_t * src):
- * '''enter src into AlignedRead.'''
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3370
+ *
+ *
+ * cdef class IndexedReads: # <<<<<<<<<<<<<<
+ * """index a bamfile by read.
+ *
*/
-struct __pyx_obj_9csamtools_AlignedRead {
+struct __pyx_obj_9csamtools_IndexedReads {
PyObject_HEAD
- bam1_t *_delegate;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ samfile_t *fp;
+ PyObject *index;
+ int owns_samfile;
};
-
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1397
- * return ret
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":82
+ * return dest
+ *
+ * cdef class PileupProxy # <<<<<<<<<<<<<<
+ * cdef makePileupProxy( bam_pileup1_t * plp, int tid, int pos, int n ):
+ * cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
+ */
+
+struct __pyx_obj_9csamtools_PileupProxy {
+ PyObject_HEAD
+ bam_pileup1_t *plp;
+ int tid;
+ int pos;
+ int n_pu;
+};
+
+
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1542
+ * return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
* '''abstract base class for iterators over columns.
static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1567
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1712
* self.iterdata.seq = NULL
*
* cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2662
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2873
*
*
* cdef class SNPCallerBase: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_SNPCallerBase *__pyx_vtabptr_9csamtools_SNPCallerBase;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2810
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":3021
* return call
*
* cdef class SNPCaller( SNPCallerBase ): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_SNPCaller *__pyx_vtabptr_9csamtools_SNPCaller;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1144
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1206
* pass
*
* cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1596
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1402
+ * raise StopIteration
+ *
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile)*
+ *
+ */
+
+struct __pyx_vtabstruct_9csamtools_IteratorRowSelection {
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
+};
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection;
+
+
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1741
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":393
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":415
*
*
* cdef class Samfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode='r', template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
+ * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
*
*/
bam_header_t *(*_buildHeader)(struct __pyx_obj_9csamtools_Samfile *, PyObject *);
bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_Samfile *);
int (*cnext)(struct __pyx_obj_9csamtools_Samfile *);
+ int (*write)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch);
+ char *(*_getrname)(struct __pyx_obj_9csamtools_Samfile *, int);
};
static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":222
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":244
* ## Public methods
* ######################################################################
* cdef class Fastafile: # <<<<<<<<<<<<<<
static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1224
- * samclose( self.fp )
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":1292
+ * if self.owns_samfile: samclose( self.fp )
*
* cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
* """*(Samfile samfile, int reopen = True)*
static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2735
+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2946
* sys.stdout.flush()
*
* cdef class IteratorSNPCalls( SNPCallerBase ): # <<<<<<<<<<<<<<
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact); /*proto*/
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObject* default_value) {
PyObject* value;
#if PY_MAJOR_VERSION >= 3
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t);
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
+
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t);
static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*proto*/
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t);
+
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
static void __Pyx_WriteUnraisable(const char *name); /*proto*/
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
-
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
static PyTypeObject *__pyx_ptype_9csamtools_file = 0;
static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndelCallerBase = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndelCaller = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorIndelCalls = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
static char *__pyx_v_9csamtools_bam_nt16_rev_table;
static int __pyx_v_9csamtools_max_pos;
static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
static PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IOError;
+static PyObject *__pyx_builtin_OverflowError;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_StopIteration;
static char __pyx_k_16[] = "unequal names and lengths of reference sequences";
static char __pyx_k_17[] = "-";
static char __pyx_k_18[] = "file `%s` not found";
-static char __pyx_k_19[] = "could not open file - is it SAM/BAM format?";
-static char __pyx_k_20[] = ".bai";
-static char __pyx_k_21[] = "error while opening index `%s` ";
-static char __pyx_k_22[] = "tid out of range 0<=tid<%i";
-static char __pyx_k_23[] = "[:-]";
-static char __pyx_k_24[] = "invalid reference `%s`";
-static char __pyx_k_25[] = "invalid coordinates: start (%i) > end (%i)";
-static char __pyx_k_26[] = "seek only available in bam files";
-static char __pyx_k_28[] = "fetch called on bamfile without index";
-static char __pyx_k_29[] = "callback functionality requires a region/reference";
-static char __pyx_k_30[] = "no index available for fetch";
-static char __pyx_k_31[] = "fetch called for samfile without header";
-static char __pyx_k_32[] = "fetch for a region is not available for sam files";
-static char __pyx_k_33[] = "callback not implemented yet";
-static char __pyx_k_34[] = "read is unpaired";
-static char __pyx_k_35[] = "mate is unmapped";
-static char __pyx_k_36[] = "mate not found";
-static char __pyx_k_38[] = "counting functionality requires a region/reference";
-static char __pyx_k_39[] = "count for a region is not available for sam files";
-static char __pyx_k_40[] = "no index available for pileup";
-static char __pyx_k_41[] = "pileup of samfiles not implemented yet";
-static char __pyx_k_42[] = "@";
-static char __pyx_k_43[] = "header line without '@': '%s'";
-static char __pyx_k_44[] = "header line with invalid type '%s': '%s'";
-static char __pyx_k_45[] = ":";
-static char __pyx_k_46[] = "unknown field code '%s' in record '%s'";
-static char __pyx_k_47[] = "multiple '%s' lines are not permitted";
-static char __pyx_k_48[] = "@%s";
-static char __pyx_k_49[] = "%s:%s";
-static char __pyx_k_50[] = "invalid type for record %s: %s, expected %s";
-static char __pyx_k_51[] = "incomplete sequence information in '%s'";
-static char __pyx_k_52[] = "no index available for iteration";
-static char __pyx_k_53[] = "reference sequence for '%s' (tid=%i) not found";
-static char __pyx_k_54[] = "unknown stepper option `%s` in IteratorColumn";
-static char __pyx_k_56[] = "error during iteration";
-static char __pyx_k_57[] = "Invalid clipping in CIGAR string";
-static char __pyx_k_58[] = "quality and sequence mismatch: %i != %i";
-static char __pyx_k_59[] = "%c";
-static char __pyx_k_60[] = "create_string_buffer";
-static char __pyx_k_61[] = "<cccf";
-static char __pyx_k_62[] = "<cccb";
-static char __pyx_k_63[] = "<ccch";
-static char __pyx_k_64[] = "integer %i out of range of BAM/SAM specification";
-static char __pyx_k_65[] = "<ccci";
-static char __pyx_k_66[] = "<cccB";
-static char __pyx_k_67[] = "<cccH";
-static char __pyx_k_68[] = "<cccI";
-static char __pyx_k_69[] = "<cccc";
-static char __pyx_k_70[] = "<ccc%is";
-static char __pyx_k_71[] = "tags field too large";
-static char __pyx_k_72[] = "tag '%s' not present";
-static char __pyx_k_73[] = "Contig index";
-static char __pyx_k_74[] = "Mapped position on contig";
-static char __pyx_k_75[] = "Contig index for mate pair";
-static char __pyx_k_76[] = "Position of mate pair";
-static char __pyx_k_77[] = "Insert size";
-static char __pyx_k_78[] = "Binary flag";
-static char __pyx_k_79[] = "Count of cigar entries";
-static char __pyx_k_80[] = "Cigar entries";
-static char __pyx_k_81[] = "Mapping quality";
-static char __pyx_k_82[] = "Bam index bin number";
-static char __pyx_k_83[] = "Length of query name";
-static char __pyx_k_84[] = "Query name";
-static char __pyx_k_85[] = "Length of query sequence";
-static char __pyx_k_86[] = "Query sequence";
-static char __pyx_k_87[] = "Quality scores";
-static char __pyx_k_88[] = "Length of auxilary data";
-static char __pyx_k_89[] = "Maximum data length";
-static char __pyx_k_90[] = "Current data length";
-static char __pyx_k_91[] = "%-30s %-10s= %s";
-static char __pyx_k_92[] = "(";
-static char __pyx_k_93[] = ")";
-static char __pyx_k_94[] = "This class cannot be instantiated from Python";
-static char __pyx_k_97[] = "No such file or directory: '%s'";
-static char __pyx_k_98[] = "-o";
-static char __pyx_k_99[] = "option -o is forbidden in samtools view";
+static char __pyx_k_19[] = "could not open file (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_20[] = "file does not have valid header (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_21[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_22[] = ".bai";
+static char __pyx_k_23[] = "error while opening index `%s` ";
+static char __pyx_k_24[] = "tid %i out of range 0<=tid<%i";
+static char __pyx_k_25[] = "[:-]";
+static char __pyx_k_26[] = "invalid reference `%s`";
+static char __pyx_k_27[] = "invalid coordinates: start (%i) > end (%i)";
+static char __pyx_k_28[] = "seek only available in bam files";
+static char __pyx_k_30[] = "fetch called on bamfile without index";
+static char __pyx_k_31[] = "callback functionality requires a region/reference";
+static char __pyx_k_32[] = "no index available for fetch";
+static char __pyx_k_33[] = "fetch called for samfile without header";
+static char __pyx_k_34[] = "fetch for a region is not available for sam files";
+static char __pyx_k_35[] = "callback not implemented yet";
+static char __pyx_k_36[] = "read %s: is unpaired";
+static char __pyx_k_37[] = "mate %s: is unmapped";
+static char __pyx_k_38[] = "mate not found";
+static char __pyx_k_40[] = "counting functionality requires a region/reference";
+static char __pyx_k_41[] = "count for a region is not available for sam files";
+static char __pyx_k_42[] = "no index available for pileup";
+static char __pyx_k_43[] = "pileup of samfiles not implemented yet";
+static char __pyx_k_44[] = "@";
+static char __pyx_k_45[] = "header line without '@': '%s'";
+static char __pyx_k_46[] = "header line with invalid type '%s': '%s'";
+static char __pyx_k_47[] = ":";
+static char __pyx_k_48[] = "unknown field code '%s' in record '%s'";
+static char __pyx_k_49[] = "multiple '%s' lines are not permitted";
+static char __pyx_k_50[] = "@%s";
+static char __pyx_k_51[] = "%s:%s";
+static char __pyx_k_52[] = "invalid type for record %s: %s, expected %s";
+static char __pyx_k_53[] = "incomplete sequence information in '%s'";
+static char __pyx_k_54[] = "no index available for iteration";
+static char __pyx_k_55[] = "can only use this iterator on bam files";
+static char __pyx_k_56[] = "reference sequence for '%s' (tid=%i) not found";
+static char __pyx_k_57[] = "unknown stepper option `%s` in IteratorColumn";
+static char __pyx_k_59[] = "error during iteration";
+static char __pyx_k_60[] = "Invalid clipping in CIGAR string";
+static char __pyx_k_61[] = "quality and sequence mismatch: %i != %i";
+static char __pyx_k_62[] = "%c";
+static char __pyx_k_63[] = "create_string_buffer";
+static char __pyx_k_64[] = "<cccf";
+static char __pyx_k_65[] = "<cccb";
+static char __pyx_k_66[] = "<ccch";
+static char __pyx_k_67[] = "integer %i out of range of BAM/SAM specification";
+static char __pyx_k_68[] = "<ccci";
+static char __pyx_k_69[] = "<cccB";
+static char __pyx_k_70[] = "<cccH";
+static char __pyx_k_71[] = "<cccI";
+static char __pyx_k_72[] = "<cccc";
+static char __pyx_k_73[] = "<ccc%is";
+static char __pyx_k_74[] = "tags field too large";
+static char __pyx_k_75[] = "tag '%s' not present";
+static char __pyx_k_76[] = "Contig index";
+static char __pyx_k_77[] = "Mapped position on contig";
+static char __pyx_k_78[] = "Contig index for mate pair";
+static char __pyx_k_79[] = "Position of mate pair";
+static char __pyx_k_80[] = "Insert size";
+static char __pyx_k_81[] = "Binary flag";
+static char __pyx_k_82[] = "Count of cigar entries";
+static char __pyx_k_83[] = "Cigar entries";
+static char __pyx_k_84[] = "Mapping quality";
+static char __pyx_k_85[] = "Bam index bin number";
+static char __pyx_k_86[] = "Length of query name";
+static char __pyx_k_87[] = "Query name";
+static char __pyx_k_88[] = "Length of query sequence";
+static char __pyx_k_89[] = "Query sequence";
+static char __pyx_k_90[] = "Quality scores";
+static char __pyx_k_91[] = "Length of auxilary data";
+static char __pyx_k_92[] = "Maximum data length";
+static char __pyx_k_93[] = "Current data length";
+static char __pyx_k_94[] = "%-30s %-10s= %s";
+static char __pyx_k_95[] = "(";
+static char __pyx_k_96[] = ")";
+static char __pyx_k_97[] = "This class cannot be instantiated from Python";
static char __pyx_k__A[] = "A";
static char __pyx_k__C[] = "C";
static char __pyx_k__D[] = "D";
static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
static char __pyx_k__x[] = "x";
-static char __pyx_k_100[] = "_rms_mapping_quality";
-static char __pyx_k_101[] = "--> read %i %s %i";
-static char __pyx_k_102[] = "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i";
-static char __pyx_k_103[] = "-------------------------------------\n";
-static char __pyx_k_104[] = "IteratorSNPCalls requires an pileup iterator with reference sequence";
-static char __pyx_k_105[] = "position %i out of bounds on reference sequence (len=%i)";
-static char __pyx_k_106[] = "no reads in region - no call";
-static char __pyx_k_107[] = "%s/%s";
-static char __pyx_k_108[] = "IndelCallerBase requires an pileup iterator with reference sequence";
-static char __pyx_k_109[] = "the query name (None if not present)";
-static char __pyx_k_110[] = "the :term:`cigar` alignment (None if not present).\n ";
-static char __pyx_k_111[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_112[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
-static char __pyx_k_113[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present)\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
-static char __pyx_k_114[] = "aligned query sequence quality values (None if not present)";
-static char __pyx_k_115[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
-static char __pyx_k_116[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
-static char __pyx_k_117[] = "Length of the aligned query sequence";
-static char __pyx_k_118[] = "the tags in the AUX field.\n\n This property permits convenience access to \n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a \n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n ";
-static char __pyx_k_119[] = "properties flag";
-static char __pyx_k_120[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_121[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
-static char __pyx_k_122[] = "0-based leftmost coordinate";
-static char __pyx_k_123[] = "properties bin";
-static char __pyx_k_124[] = "length of the read (read only). Returns 0 if not given.";
-static char __pyx_k_125[] = "aligned end position of the read (read only). Returns\n None if not available.";
-static char __pyx_k_126[] = "aligned length of the read (read only). Returns None if\n not available.";
-static char __pyx_k_127[] = "mapping quality";
-static char __pyx_k_128[] = "the :term:`reference` id of the mate ";
-static char __pyx_k_129[] = "the position of the mate";
-static char __pyx_k_130[] = "the insert size";
-static char __pyx_k_131[] = "true if read is paired in sequencing";
-static char __pyx_k_132[] = "true if read is mapped in a proper pair";
-static char __pyx_k_133[] = "true if read itself is unmapped";
-static char __pyx_k_134[] = "true if the mate is unmapped";
-static char __pyx_k_135[] = "true if read is mapped to reverse strand";
-static char __pyx_k_136[] = "true is read is mapped to reverse strand";
-static char __pyx_k_137[] = "true if this is read1";
-static char __pyx_k_138[] = "true if this is read2";
-static char __pyx_k_139[] = "true if not primary alignment";
-static char __pyx_k_140[] = "true if QC failure";
-static char __pyx_k_141[] = " true if optical or PCR duplicate";
-static char __pyx_k_142[] = "the chromosome ID as is defined in the header";
-static char __pyx_k_143[] = "number of reads mapping to this column.";
-static char __pyx_k_144[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
-static char __pyx_k_145[] = "a :class:`pysam.AlignedRead` object of the aligned read";
-static char __pyx_k_146[] = "position of the read base at the pileup site, 0-based";
-static char __pyx_k_147[] = "indel length; 0 for no indel, positive for ins and negative for del";
-static char __pyx_k_148[] = "1 iff the base on the padded read is a deletion";
-static char __pyx_k_149[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_150[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_151[] = "tuple with the names of :term:`reference` sequences.";
-static char __pyx_k_152[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as \n :attr:`pysam.Samfile.references`\n ";
-static char __pyx_k_153[] = "full contents of the :term:`sam file` header as a string.";
-static char __pyx_k_154[] = "header information within the :term:`sam file`. The records and fields are returned as \n a two-level dictionary.\n ";
-static char __pyx_k_155[] = "current sequence length.";
-static char __pyx_k_156[] = "nucleotide position of SNP.";
-static char __pyx_k_157[] = "reference base at pos. ``N`` if no reference sequence supplied.";
-static char __pyx_k_158[] = "the genotype called.";
-static char __pyx_k_159[] = "the genotype quality (Phred-scaled).";
-static char __pyx_k_160[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
-static char __pyx_k_161[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
-static char __pyx_k_162[] = "coverage or read depth - the number of reads involved in the call.";
-static char __pyx_k_163[] = "sequence of first allele.";
-static char __pyx_k_164[] = "sequence of second allele.";
-static char __pyx_k_165[] = "reads supporting first allele.";
-static char __pyx_k_166[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_167[] = "/dev/null";
-static char __pyx_k_168[] = "A pileup column. A pileup column contains \n all the reads that map to a certain target base.\n\n tid \n chromosome ID as is defined in the header \n pos \n the target base coordinate (0-based) \n n \n number of reads mapping to this column \n pileups \n list of reads (:class:`pysam.PileupRead`) aligned to this column \n ";
-static char __pyx_k_169[] = "\n stderr is captured. \n ";
-static char __pyx_k_170[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
-static char __pyx_k_171[] = "Fastafile._isOpen (line 243)";
-static char __pyx_k_172[] = "Fastafile._open (line 253)";
-static char __pyx_k_173[] = "Fastafile.fetch (line 284)";
-static char __pyx_k_174[] = "Samfile._isOpen (line 451)";
-static char __pyx_k_175[] = "Samfile._hasIndex (line 455)";
-static char __pyx_k_176[] = "Samfile._open (line 459)";
-static char __pyx_k_177[] = "Samfile.getrname (line 582)";
-static char __pyx_k_178[] = "Samfile.gettid (line 590)";
-static char __pyx_k_179[] = "Samfile._parseRegion (line 599)";
-static char __pyx_k_180[] = "Samfile.seek (line 644)";
-static char __pyx_k_181[] = "Samfile.tell (line 655)";
-static char __pyx_k_182[] = "Samfile.fetch (line 666)";
-static char __pyx_k_183[] = "Samfile.mate (line 735)";
-static char __pyx_k_184[] = "Samfile.count (line 776)";
-static char __pyx_k_185[] = "Samfile.pileup (line 821)";
-static char __pyx_k_186[] = "Samfile.close (line 902)";
-static char __pyx_k_187[] = "Samfile.write (line 918)";
-static char __pyx_k_188[] = "Samfile._buildLine (line 1022)";
-static char __pyx_k_189[] = "Samfile.__next__ (line 1111)";
-static char __pyx_k_190[] = "IteratorRowRegion.__next__ (line 1213)";
-static char __pyx_k_191[] = "IteratorRowAll.__next__ (line 1266)";
-static char __pyx_k_192[] = "IteratorRowAllRefs.__next__ (line 1302)";
-static char __pyx_k_193[] = "IteratorColumn.addReference (line 1489)";
-static char __pyx_k_194[] = "IteratorColumn.hasReference (line 1497)";
-static char __pyx_k_195[] = "IteratorColumnRegion.__next__ (line 1579)";
-static char __pyx_k_196[] = "IteratorColumnRegion";
-static char __pyx_k_197[] = "IteratorColumnAllRefs.__next__ (line 1610)";
-static char __pyx_k_198[] = "IteratorColumnAllRefs";
-static char __pyx_k_199[] = "AlignedRead.__str__ (line 1759)";
-static char __pyx_k_200[] = "AlignedRead.compare (line 1772)";
-static char __pyx_k_201[] = "AlignedRead.opt (line 2331)";
-static char __pyx_k_202[] = "AlignedRead.fancy_str (line 2353)";
-static char __pyx_k_203[] = "Outs.setdevice (line 2495)";
-static char __pyx_k_204[] = "Outs.setfile (line 2500)";
-static char __pyx_k_205[] = "Outs.restore (line 2512)";
-static char __pyx_k_206[] = "_samtools_dispatch (line 2523)";
-static char __pyx_k_207[] = "IteratorSNPCalls.__next__ (line 2758)";
-static char __pyx_k_208[] = "SNPCaller.call (line 2830)";
-static char __pyx_k_209[] = "IndelCaller.call (line 3095)";
-static char __pyx_k_210[] = "IteratorIndelCalls.__next__ (line 3142)";
+static char __pyx_k_100[] = "No such file or directory: '%s'";
+static char __pyx_k_101[] = "-o";
+static char __pyx_k_102[] = "option -o is forbidden in samtools view";
+static char __pyx_k_103[] = "_rms_mapping_quality";
+static char __pyx_k_104[] = "--> read %i %s %i";
+static char __pyx_k_105[] = "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i";
+static char __pyx_k_106[] = "-------------------------------------\n";
+static char __pyx_k_107[] = "IteratorSNPCalls requires an pileup iterator with reference sequence";
+static char __pyx_k_108[] = "position %i out of bounds on reference sequence (len=%i)";
+static char __pyx_k_109[] = "no reads in region - no call";
+static char __pyx_k_110[] = "%s/%s";
+static char __pyx_k_111[] = "IndelCallerBase requires an pileup iterator with reference sequence";
+static char __pyx_k_112[] = "can only IndexReads on bam files";
+static char __pyx_k_113[] = "read %s not found";
+static char __pyx_k_114[] = "the query name (None if not present)";
+static char __pyx_k_115[] = "the :term:`cigar` alignment (None if not present).\n ";
+static char __pyx_k_116[] = "read sequence bases, including :term:`soft clipped` bases (None if not present)";
+static char __pyx_k_117[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present)";
+static char __pyx_k_118[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present)\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained.";
+static char __pyx_k_119[] = "aligned query sequence quality values (None if not present)";
+static char __pyx_k_120[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
+static char __pyx_k_121[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
+static char __pyx_k_122[] = "Length of the aligned query sequence";
+static char __pyx_k_123[] = "the tags in the AUX field.\n\n This property permits convenience access to \n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a \n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n ";
+static char __pyx_k_124[] = "properties flag";
+static char __pyx_k_125[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
+static char __pyx_k_126[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence \n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n \n ";
+static char __pyx_k_127[] = "0-based leftmost coordinate";
+static char __pyx_k_128[] = "properties bin";
+static char __pyx_k_129[] = "length of the read (read only). Returns 0 if not given.";
+static char __pyx_k_130[] = "aligned end position of the read (read only). Returns\n None if not available.";
+static char __pyx_k_131[] = "aligned length of the read (read only). Returns None if\n not available.";
+static char __pyx_k_132[] = "mapping quality";
+static char __pyx_k_133[] = "the :term:`reference` id of the mate ";
+static char __pyx_k_134[] = "the position of the mate";
+static char __pyx_k_135[] = "the insert size";
+static char __pyx_k_136[] = "true if read is paired in sequencing";
+static char __pyx_k_137[] = "true if read is mapped in a proper pair";
+static char __pyx_k_138[] = "true if read itself is unmapped";
+static char __pyx_k_139[] = "true if the mate is unmapped";
+static char __pyx_k_140[] = "true if read is mapped to reverse strand";
+static char __pyx_k_141[] = "true is read is mapped to reverse strand";
+static char __pyx_k_142[] = "true if this is read1";
+static char __pyx_k_143[] = "true if this is read2";
+static char __pyx_k_144[] = "true if not primary alignment";
+static char __pyx_k_145[] = "true if QC failure";
+static char __pyx_k_146[] = "true if optical or PCR duplicate";
+static char __pyx_k_147[] = "a list of reference positions that this read aligns to.";
+static char __pyx_k_148[] = "number of :term:`filename` associated with this object.";
+static char __pyx_k_149[] = "number of :term:`reference` sequences in the file.";
+static char __pyx_k_150[] = "tuple with the names of :term:`reference` sequences.";
+static char __pyx_k_151[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as \n :attr:`pysam.Samfile.references`\n ";
+static char __pyx_k_152[] = "full contents of the :term:`sam file` header as a string.";
+static char __pyx_k_153[] = "header information within the :term:`sam file`. The records and fields are returned as \n a two-level dictionary.\n ";
+static char __pyx_k_154[] = "the chromosome ID as is defined in the header";
+static char __pyx_k_155[] = "number of reads mapping to this column.";
+static char __pyx_k_156[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
+static char __pyx_k_157[] = "a :class:`pysam.AlignedRead` object of the aligned read";
+static char __pyx_k_158[] = "position of the read base at the pileup site, 0-based";
+static char __pyx_k_159[] = "indel length; 0 for no indel, positive for ins and negative for del";
+static char __pyx_k_160[] = "1 iff the base on the padded read is a deletion";
+static char __pyx_k_161[] = "current sequence length.";
+static char __pyx_k_162[] = "nucleotide position of SNP.";
+static char __pyx_k_163[] = "reference base at pos. ``N`` if no reference sequence supplied.";
+static char __pyx_k_164[] = "the genotype called.";
+static char __pyx_k_165[] = "the genotype quality (Phred-scaled).";
+static char __pyx_k_166[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
+static char __pyx_k_167[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
+static char __pyx_k_168[] = "coverage or read depth - the number of reads involved in the call.";
+static char __pyx_k_169[] = "sequence of first allele.";
+static char __pyx_k_170[] = "sequence of second allele.";
+static char __pyx_k_171[] = "reads supporting first allele.";
+static char __pyx_k_172[] = "=ACMGRSVTWYHKDBN";
+static char __pyx_k_173[] = "A pileup column. A pileup column contains \n all the reads that map to a certain target base.\n\n tid \n chromosome ID as is defined in the header \n pos \n the target base coordinate (0-based) \n n \n number of reads mapping to this column \n pileups \n list of reads (:class:`pysam.PileupRead`) aligned to this column \n ";
+static char __pyx_k_174[] = "\n stderr is captured. \n ";
+static char __pyx_k_175[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_176[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
+static char __pyx_k_177[] = "Fastafile._isOpen (line 265)";
+static char __pyx_k_178[] = "Fastafile._open (line 275)";
+static char __pyx_k_179[] = "Fastafile.fetch (line 306)";
+static char __pyx_k_180[] = "Samfile._isOpen (line 464)";
+static char __pyx_k_181[] = "Samfile._hasIndex (line 468)";
+static char __pyx_k_182[] = "Samfile._open (line 472)";
+static char __pyx_k_183[] = "Samfile.gettid (line 612)";
+static char __pyx_k_184[] = "Samfile.getrname (line 621)";
+static char __pyx_k_185[] = "Samfile._parseRegion (line 637)";
+static char __pyx_k_186[] = "Samfile.seek (line 691)";
+static char __pyx_k_187[] = "Samfile.tell (line 702)";
+static char __pyx_k_188[] = "Samfile.fetch (line 713)";
+static char __pyx_k_189[] = "Samfile.mate (line 782)";
+static char __pyx_k_190[] = "Samfile.count (line 825)";
+static char __pyx_k_191[] = "Samfile.pileup (line 869)";
+static char __pyx_k_192[] = "Samfile.close (line 953)";
+static char __pyx_k_193[] = "Samfile.write (line 969)";
+static char __pyx_k_194[] = "Samfile._buildLine (line 1078)";
+static char __pyx_k_195[] = "Samfile.__next__ (line 1173)";
+static char __pyx_k_196[] = "IteratorRowRegion.__next__ (line 1281)";
+static char __pyx_k_197[] = "IteratorRowAll.__next__ (line 1340)";
+static char __pyx_k_198[] = "IteratorRowAllRefs.__next__ (line 1375)";
+static char __pyx_k_199[] = "IteratorRowSelection.__next__ (line 1459)";
+static char __pyx_k_200[] = "IteratorRowSelection";
+static char __pyx_k_201[] = "IteratorColumn.addReference (line 1634)";
+static char __pyx_k_202[] = "IteratorColumn.hasReference (line 1642)";
+static char __pyx_k_203[] = "IteratorColumnRegion.__next__ (line 1724)";
+static char __pyx_k_204[] = "IteratorColumnRegion";
+static char __pyx_k_205[] = "IteratorColumnAllRefs.__next__ (line 1755)";
+static char __pyx_k_206[] = "IteratorColumnAllRefs";
+static char __pyx_k_207[] = "AlignedRead.__str__ (line 1903)";
+static char __pyx_k_208[] = "AlignedRead.compare (line 1928)";
+static char __pyx_k_209[] = "AlignedRead.overlap (line 2512)";
+static char __pyx_k_210[] = "AlignedRead.opt (line 2541)";
+static char __pyx_k_211[] = "AlignedRead.fancy_str (line 2563)";
+static char __pyx_k_212[] = "Outs.setdevice (line 2705)";
+static char __pyx_k_213[] = "Outs.setfile (line 2710)";
+static char __pyx_k_214[] = "Outs.restore (line 2723)";
+static char __pyx_k_215[] = "_samtools_dispatch (line 2734)";
+static char __pyx_k_216[] = "IteratorSNPCalls.__next__ (line 2969)";
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static char __pyx_k__mate[] = "mate";
static char __pyx_k__mode[] = "mode";
static char __pyx_k__mpos[] = "mpos";
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static char __pyx_k__mtid[] = "mtid";
static char __pyx_k__n_pu[] = "n_pu";
static char __pyx_k__name[] = "name";
static char __pyx_k__qpos[] = "qpos";
static char __pyx_k__qseq[] = "qseq";
static char __pyx_k__qual[] = "qual";
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static char __pyx_k__seek[] = "seek";
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static char __pyx_k__tags[] = "tags";
static char __pyx_k___open[] = "_open";
static char __pyx_k___qpos[] = "_qpos";
static char __pyx_k__bqual[] = "bqual";
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static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
static char __pyx_k__cnext[] = "cnext";
static char __pyx_k__stderr[] = "stderr";
static char __pyx_k__stdout[] = "stdout";
static char __pyx_k__struct[] = "struct";
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static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__IntType[] = "IntType";
static char __pyx_k__O_CREAT[] = "O_CREAT";
static char __pyx_k__Samfile[] = "Samfile";
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static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k___is_del[] = "_is_del";
static char __pyx_k__compare[] = "compare";
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static char __pyx_k__is_head[] = "is_head";
static char __pyx_k__is_tail[] = "is_tail";
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static char __pyx_k__l_qname[] = "l_qname";
static char __pyx_k__mkstemp[] = "mkstemp";
static char __pyx_k__n_cigar[] = "n_cigar";
static char __pyx_k__options[] = "options";
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static char __pyx_k__pileups[] = "pileups";
static char __pyx_k__q_indel[] = "q_indel";
static char __pyx_k__r_indel[] = "r_indel";
static char __pyx_k__isremote[] = "isremote";
static char __pyx_k__iterdata[] = "iterdata";
static char __pyx_k__nextiter[] = "nextiter";
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static char __pyx_k__samtools[] = "samtools";
static char __pyx_k__stderr_f[] = "stderr_f";
static char __pyx_k__stderr_h[] = "stderr_h";
static char __pyx_k__exc_value[] = "exc_value";
static char __pyx_k__fancy_str[] = "fancy_str";
static char __pyx_k__fastafile[] = "fastafile";
-static char __pyx_k__is_paired[] = "is_paired";
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static char __pyx_k__max_depth[] = "max_depth";
static char __pyx_k__min_baseQ[] = "min_baseQ";
static char __pyx_k__n_targets[] = "n_targets";
static char __pyx_k__pack_into[] = "pack_into";
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static char __pyx_k__readlines[] = "readlines";
static char __pyx_k__reference[] = "reference";
static char __pyx_k__setdevice[] = "setdevice";
static char __pyx_k__PileupProxy[] = "PileupProxy";
static char __pyx_k__StderrStore[] = "StderrStore";
static char __pyx_k__collections[] = "collections";
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static char __pyx_k__getSequence[] = "getSequence";
static char __pyx_k__nreferences[] = "nreferences";
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static char __pyx_k__snp_quality[] = "snp_quality";
static char __pyx_k__stderr_save[] = "stderr_save";
static char __pyx_k__target_name[] = "target_name";
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static char __pyx_k__PileupColumn[] = "PileupColumn";
static char __pyx_k___buildHeader[] = "_buildHeader";
static char __pyx_k___parseRegion[] = "_parseRegion";
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static char __pyx_k__hasReference[] = "hasReference";
static char __pyx_k__n_haplotypes[] = "n_haplotypes";
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static char __pyx_k__reads_second[] = "reads_second";
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static char __pyx_k__StopIteration[] = "StopIteration";
static char __pyx_k__VALID_HEADERS[] = "VALID_HEADERS";
static char __pyx_k__second_allele[] = "second_allele";
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static char __pyx_k__referencelengths[] = "referencelengths";
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static char __pyx_k__consensus_quality[] = "consensus_quality";
static char __pyx_k__setupIteratorData[] = "setupIteratorData";
static char __pyx_k__IteratorIndelCalls[] = "IteratorIndelCalls";
static char __pyx_k__IteratorRowAllRefs[] = "IteratorRowAllRefs";
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static char __pyx_k__VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER";
static char __pyx_k__VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES";
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static PyObject *__pyx_n_s__IOError;
static PyObject *__pyx_n_s__IndelCaller;
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static PyObject *__pyx_n_s__IntType;
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static PyObject *__pyx_n_s__O_CREAT;
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static PyObject *__pyx_n_s__Outs;
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static PyObject *__pyx_n_s__StderrStore;
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static PyObject *__pyx_n_s__StopIteration;
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static PyObject *__pyx_n_s__VALID_HEADER_TYPES;
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static PyObject *__pyx_n_s__pileup_iter;
static PyObject *__pyx_n_s__pileups;
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static PyObject *__pyx_n_s__q_cns;
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static PyObject *__pyx_pf_9csamtools_7Samfile_mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
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- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":748
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*
* '''
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- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":1754
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__Pyx_GOTREF(__pyx_t_5);
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* self.cigar,
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- * self.seq,
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+/* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2919
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+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2922
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pysam_dump_glf(__pyx_v_g, __pyx_v_self->c);
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2712
+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2923
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- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2713
+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2924
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+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2925
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__Pyx_GOTREF(((PyObject *)__pyx_t_4));
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+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2931
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__Pyx_GOTREF(__pyx_t_5);
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+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2932
* print "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i" \
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__Pyx_GOTREF(__pyx_t_6);
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+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2933
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__Pyx_GOTREF(__pyx_t_4);
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2723
+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2934
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+ __pyx_t_3 = PyInt_FromLong(__pyx_v_self->iter->n_plp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2724
+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2935
* self.c.q_r,
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* self.iter.n_plp, # <<<<<<<<<<<<<<
* rb,
* cns >> 8 & 0xff,
*/
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+ __pyx_t_7 = PyInt_FromLong(__pyx_v_self->iter->n_plp); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2935; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
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+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2936
* self.iter.n_plp,
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* cns >> 16 & 0xff,
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+ __pyx_t_8 = PyInt_FromLong(__pyx_v_rb); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2726
+ /* "/ifs/devel/pysam/pysam/pysam/csamtools.pyx":2937
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* cns >> 8 & 0xff, # <<<<<<<<<<<<<<
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__Pyx_GOTREF(__pyx_t_9);
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/csamtools.pyx":2727
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+ {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_139), 0},
+ {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_140), 0},
+ {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_141), 0},
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+ {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_146), 0},
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{0, 0, 0, 0, 0}
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&__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
__pyx_pf_9csamtools_11AlignedRead___hash__, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_11AlignedRead___str__, /*tp_str*/
+ __pyx_pf_9csamtools_11AlignedRead___str__, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("AlignedRead()\n\n Class representing an aligned read. see SAM format specification for \n the meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+static struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile;
+
+static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Samfile *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools_Samfile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
+ if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pf_9csamtools_7Samfile___dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
+}
+
+static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__isOpen)},
+ {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__hasIndex)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__open)},
+ {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_gettid)},
+ {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_getrname)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__parseRegion)},
+ {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_seek)},
+ {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_tell)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_fetch)},
+ {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_mate)},
+ {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_count)},
+ {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_pileup)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_close)},
+ {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_write)},
+ {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___enter__)},
+ {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___exit__)},
+ {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__buildLine)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___next__)},
+ {0, 0, 0, 0}
+};
+
+static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_148), 0},
+ {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_149), 0},
+ {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_150), 0},
+ {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_151), 0},
+ {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_152), 0},
+ {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_153), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_Samfile = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_Samfile = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_Samfile = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_9csamtools_Samfile = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_Samfile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Samfile, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("\n Class representing an aligned read. see SAM format specification for meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*\n \n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n \n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary \n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output. \n Use ``h`` to output header information in text (:term:`TAM`) mode.\n\n If ``b`` is present, it must immediately follow ``r`` or ``w``. \n Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open \n a :term:`BAM` formatted file for reading, type::\n\n f = pysam.Samfile('ex1.bam','rb')\n\n If mode is not specified, we will try to auto-detect in the order 'r', 'rb', thus both the following\n should work::\n\n f1 = pysam.Samfile('ex1.bam' )\n f2 = pysam.Samfile('ex1.bam' )\n\n If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n sources (see also the samtools format specification):\n\n 1. If *template* is given, the header is copied from a another *Samfile* \n (*template* must be of type *Samfile*).\n\n 2. If *header* is given, the header is built from a multi-level dictionary. The first level \n are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line \n being a list of tag-value pairs.\n\n 3. If *text* is given, new header text is copied from raw text.\n\n 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. \n\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
+ __pyx_pf_9csamtools_7Samfile___iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_7Samfile___next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_Samfile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
+ __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
+ 0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
+ __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
};
static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
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- {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_143), 0},
+ {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
+ {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_155), 0},
{(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
- {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_144), 0},
+ {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_156), 0},
{0, 0, 0, 0, 0}
};
0, /*tp_setattro*/
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- __Pyx_DOCSTR("A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column \n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("PileupProxy()\nA pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column \n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
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- {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_146), 0},
- {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_147), 0},
- {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_148), 0},
+ {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_157), 0},
+ {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_158), 0},
+ {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_159), 0},
+ {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_160), 0},
{(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0},
{(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0},
{(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0},
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("A read aligned to a column.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
__pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/
__pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/
0, /*tp_richcompare*/
}
static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
-}
-
-static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__open)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_close, METH_NOARGS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_fetch)},
- {0, 0, 0, 0}
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-
-static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
- {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_149), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_Fastafile = {
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- 0, /*nb_subtract*/
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- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
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- 0, /*nb_divmod*/
- 0, /*nb_power*/
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- 0, /*nb_xor*/
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- #if PY_MAJOR_VERSION < 3
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- #if PY_MAJOR_VERSION < 3
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- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
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- 0, /*nb_index*/
- #endif
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-static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
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- 0, /*sq_repeat*/
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- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
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- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
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-
-static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pf_9csamtools_9Fastafile___len__, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
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- 0, /*bf_getsegcount*/
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- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
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-PyTypeObject __pyx_type_9csamtools_Fastafile = {
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- __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_Fastafile, /*tp_as_number*/
- &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Fastafile, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("*(filename)*\n \n A *FASTA* file. The file is automatically opened.\n\n The file expects an indexed fasta file.\n\n TODO: \n add automatic indexing.\n add function to get sequence names.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
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-
-static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_Samfile *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_Samfile *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
- if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
- return o;
-}
-
-static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_7Samfile___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
-}
-
-static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__open)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_getrname)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_gettid)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__parseRegion)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___enter__, METH_NOARGS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile__buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile__buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile___next__)},
+ return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
+}
+
+static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__isOpen)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile__open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile__open)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_close)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_fetch)},
{0, 0, 0, 0}
};
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- {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_151), 0},
- {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_152), 0},
- {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_153), 0},
- {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_148), 0},
{0, 0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_Samfile = {
+static PyNumberMethods __pyx_tp_as_number_Fastafile = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_Samfile = {
- 0, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
+ __pyx_pf_9csamtools_9Fastafile___len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_Samfile = {
- 0, /*mp_length*/
+static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
+ __pyx_pf_9csamtools_9Fastafile___len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
+static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_Samfile = {
+PyTypeObject __pyx_type_9csamtools_Fastafile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
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- &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Samfile, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Fastafile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Fastafile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Fastafile, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("*(filename, mode='r', template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*\n \n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n \n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode so for binary \n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output. \n Use ``h`` to output header information in text (:term:`TAM`) mode.\n\n If ``b`` is present, it must immediately follow ``r`` or ``w``. \n Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open \n a :term:`BAM` formatted file for reading, type::\n\n import pysam\n f = pysam.Samfile('ex1.bam','rb')\n\n If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n sources (see also the samtools format specification):\n\n 1. If *template* is given, the header is copied from a another *Samfile* \n (*template* must be of type *Samfile*).\n\n 2. If *header* is given, the header is built from a multi-level dictionary. The first level \n are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line \n being a list of tag-value pairs.\n\n 3. If *text* is given, new header text is copied from raw text.\n\n 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. \n\n "), /*tp_doc*/
+ __Pyx_DOCSTR("*(filename)*\n \n A *FASTA* file. The file is automatically opened.\n\n The file expects an indexed fasta file.\n\n TODO: \n add automatic indexing.\n add function to get sequence names.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_7Samfile___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_7Samfile___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_Samfile, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
+ __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
+ __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between \n samfile and the iterator.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between \n samfile and the iterator.\n "), /*tp_doc*/
__pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
__pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ __pyx_pf_9csamtools_14IteratorRowAll___iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorRowAll___next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->rowiter));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+}
+
+static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->rowiter) {
+ e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ PyObject* tmp;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->rowiter);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
+ {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_nextiter)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs___next__)},
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
+PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_14IteratorRowAll___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_14IteratorRowAll___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs___iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs___next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p;
PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
+ p->positions = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(((PyObject *)p->rowiter));
+static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pf_9csamtools_20IteratorRowSelection___dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_XDECREF(p->positions);
__pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
}
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
- }
- if (p->rowiter) {
- e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
+ if (p->positions) {
+ e = (*v)(p->positions, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
PyObject* tmp;
if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
__pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
}
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->rowiter);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ tmp = ((PyObject*)p->positions);
+ p->positions = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_nextiter, METH_NOARGS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs___next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection___next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
+PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
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- &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
+ __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
+ __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs___iter__, /*tp_iter*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs___next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
+ __pyx_pf_9csamtools_20IteratorRowSelection___iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_20IteratorRowSelection___next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
};
static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
- {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_155), 0},
+ {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_161), 0},
{0, 0, 0, 0, 0}
};
};
static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
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- {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_156), 0},
- {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_157), 0},
- {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_158), 0},
- {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_159), 0},
- {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_160), 0},
- {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_161), 0},
- {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_162), 0},
+ {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_154), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_162), 0},
+ {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_163), 0},
+ {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_164), 0},
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/*--- Initialize various global constants etc. ---*/
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+ 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_csamtools) {
- if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ 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 ---*/
- if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- __pyx_ptype_9csamtools_file = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "file", sizeof(PyFileObject), 0); if (unlikely(!__pyx_ptype_9csamtools_file)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_file = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "file", sizeof(PyFileObject), 0); if (unlikely(!__pyx_ptype_9csamtools_file)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_11AlignedRead___str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_11AlignedRead___str__.doc = __pyx_doc_9csamtools_11AlignedRead___str__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead___str__;
}
}
- if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
- __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
- #else
- *(void(**)(void))&__pyx_vtable_9csamtools_Fastafile._fetch = (void(*)(void))__pyx_f_9csamtools_9Fastafile__fetch;
- #endif
- if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
__pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
#if PY_MAJOR_VERSION >= 3
__pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
__pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
__pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
+ __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
+ __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname;
#else
*(void(**)(void))&__pyx_vtable_9csamtools_Samfile._buildHeader = (void(*)(void))__pyx_f_9csamtools_7Samfile__buildHeader;
*(void(**)(void))&__pyx_vtable_9csamtools_Samfile.getCurrent = (void(*)(void))__pyx_f_9csamtools_7Samfile_getCurrent;
*(void(**)(void))&__pyx_vtable_9csamtools_Samfile.cnext = (void(*)(void))__pyx_f_9csamtools_7Samfile_cnext;
+ *(void(**)(void))&__pyx_vtable_9csamtools_Samfile.write = (void(*)(void))__pyx_f_9csamtools_7Samfile_write;
+ *(void(**)(void))&__pyx_vtable_9csamtools_Samfile._getrname = (void(*)(void))__pyx_f_9csamtools_7Samfile__getrname;
#endif
- if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_7Samfile___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_7Samfile___next__.doc = __pyx_doc_9csamtools_7Samfile___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile___next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
+ __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
+ #if PY_MAJOR_VERSION >= 3
+ __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
+ #else
+ *(void(**)(void))&__pyx_vtable_9csamtools_Fastafile._fetch = (void(*)(void))__pyx_f_9csamtools_9Fastafile__fetch;
+ #endif
+ if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
__pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
#if PY_MAJOR_VERSION >= 3
*(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowRegion.cnext = (void(*)(void))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
#endif
__pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion___next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
__pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll;
#if PY_MAJOR_VERSION >= 3
*(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowAll.cnext = (void(*)(void))__pyx_f_9csamtools_14IteratorRowAll_cnext;
#endif
__pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_14IteratorRowAll___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_14IteratorRowAll___next__.doc = __pyx_doc_9csamtools_14IteratorRowAll___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll___next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
__pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs___next__;
}
}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
+ __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
+ #if PY_MAJOR_VERSION >= 3
+ __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
+ #else
+ *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
+ *(void(**)(void))&__pyx_vtable_9csamtools_IteratorRowSelection.cnext = (void(*)(void))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
+ #endif
+ __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection___next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection___next__;
+ }
+ }
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
__pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
#if PY_MAJOR_VERSION >= 3
__pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
*(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
*(void(**)(void))&__pyx_vtable_9csamtools_IteratorColumn.reset = (void(*)(void))__pyx_f_9csamtools_14IteratorColumn_reset;
#endif
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
__pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
__pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
__pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion___next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion;
__pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs;
__pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
__pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs___next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs;
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
__pyx_vtabptr_9csamtools_SNPCallerBase = &__pyx_vtable_9csamtools_SNPCallerBase;
#if PY_MAJOR_VERSION >= 3
#else
*(void(**)(void))&__pyx_vtable_9csamtools_SNPCallerBase.__dump = (void(*)(void))__pyx_f_9csamtools_13SNPCallerBase___dump;
#endif
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCallerBase.tp_dict, __pyx_vtabptr_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCallerBase", (PyObject *)&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCallerBase.tp_dict, __pyx_vtabptr_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SNPCallerBase", (PyObject *)&__pyx_type_9csamtools_SNPCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_SNPCallerBase = &__pyx_type_9csamtools_SNPCallerBase;
__pyx_vtabptr_9csamtools_IteratorSNPCalls = &__pyx_vtable_9csamtools_IteratorSNPCalls;
__pyx_vtable_9csamtools_IteratorSNPCalls.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase;
__pyx_type_9csamtools_IteratorSNPCalls.tp_base = __pyx_ptype_9csamtools_SNPCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__.doc = __pyx_doc_9csamtools_16IteratorSNPCalls___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_16IteratorSNPCalls___next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorSNPCalls.tp_dict, __pyx_vtabptr_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorSNPCalls", (PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorSNPCalls.tp_dict, __pyx_vtabptr_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorSNPCalls", (PyObject *)&__pyx_type_9csamtools_IteratorSNPCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IteratorSNPCalls = &__pyx_type_9csamtools_IteratorSNPCalls;
__pyx_vtabptr_9csamtools_SNPCaller = &__pyx_vtable_9csamtools_SNPCaller;
__pyx_vtable_9csamtools_SNPCaller.__pyx_base = *__pyx_vtabptr_9csamtools_SNPCallerBase;
__pyx_type_9csamtools_SNPCaller.tp_base = __pyx_ptype_9csamtools_SNPCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCaller.tp_dict, __pyx_vtabptr_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCaller", (PyObject *)&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_SNPCaller.tp_dict, __pyx_vtabptr_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SNPCaller", (PyObject *)&__pyx_type_9csamtools_SNPCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_SNPCaller = &__pyx_type_9csamtools_SNPCaller;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCall", (PyObject *)&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IndelCall", (PyObject *)&__pyx_type_9csamtools_IndelCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IndelCall = &__pyx_type_9csamtools_IndelCall;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCallerBase", (PyObject *)&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IndelCallerBase", (PyObject *)&__pyx_type_9csamtools_IndelCallerBase) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IndelCallerBase = &__pyx_type_9csamtools_IndelCallerBase;
__pyx_type_9csamtools_IndelCaller.tp_base = __pyx_ptype_9csamtools_IndelCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3076; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndelCaller", (PyObject *)&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3076; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IndelCaller", (PyObject *)&__pyx_type_9csamtools_IndelCaller) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_IndelCaller = &__pyx_type_9csamtools_IndelCaller;
__pyx_type_9csamtools_IteratorIndelCalls.tp_base = __pyx_ptype_9csamtools_IndelCallerBase;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorIndelCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorIndelCalls) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorIndelCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorIndelCalls, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__.doc = __pyx_doc_9csamtools_18IteratorIndelCalls___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorIndelCalls___next__;
}
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+ const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint64_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint64_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint64_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint64_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint64_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ return (uint64_t)-1;
+ }
+}
+
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;
#endif
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t val) {
+ const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(uint64_t) == sizeof(char)) ||
+ (sizeof(uint64_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(uint64_t) == sizeof(int)) ||
+ (sizeof(uint64_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(uint64_t),
+ little, !is_unsigned);
+ }
+}
+
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;
}
}
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
- const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint64_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint64_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint64_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint64_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- uint64_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (uint64_t)-1;
- }
-}
-
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
-
cdef extern from "string.h":
ctypedef int size_t
void *memcpy(void *dst,void *src,size_t len)
ctypedef int uint8_t
ctypedef int uint64_t
-
cdef extern from "bam.h":
# constants
uint32_t bam_calend(bam1_core_t *c, uint32_t *cigar)
+cdef extern from *:
+ ctypedef char* const_char_ptr "const char*"
+
cdef extern from "sam.h":
ctypedef struct samfile_t_un:
samfile_t_un x
bam_header_t *header
- samfile_t *samopen( char *fn, char * mode, void *aux)
+ samfile_t *samopen( const_char_ptr fn, char * mode, void *aux)
int sampileup( samfile_t *fp, int mask, bam_pileup_f func, void *data)
ctypedef struct glf1_t:
pass
-# unsigned char ref_base, dummy
-# unsigned char max_mapQ
-# unsigned char lk[10]
-# unsigned int min_lk, depth
-# unsigned char ref_base:4, dummy:4
-# unsigned char max_mapQ
-# unsigned char lk[10]
-# unsigned min_lk:8, depth:24;
-
-
cdef extern from "bam_maqcns.h":
ctypedef struct bam_maqcns_t:
uint32_t pysam_glf_depth( glf1_t * g )
void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
+
+# need to declare all C fields and methods here
+cdef class AlignedRead:
+
+ # object that this AlignedRead represents
+ cdef bam1_t * _delegate
+
+cdef class Samfile:
+ cdef char * _filename
+ # pointer to samfile
+ cdef samfile_t * samfile
+ # pointer to index
+ cdef bam_index_t *index
+ # true if file is a bam file
+ cdef int isbam
+ # true if file is not on the local filesystem
+ cdef int isremote
+ # current read within iteration
+ cdef bam1_t * b
+ # file opening mode
+ cdef char * mode
+
+ cdef bam_header_t * _buildHeader( self, new_header )
+ cdef bam1_t * getCurrent( self )
+ cdef int cnext(self)
+
+ # write an aligned read
+ cpdef int write( self, AlignedRead read )
+
+ cdef char * _getrname( self, int tid )
+
- # cython: embedsignature=True
+# cython: embedsignature=True
# cython: profile=True
# adds doc-strings for sphinx
-import tempfile, os, sys, types, struct, ctypes, collections, re
-
+import tempfile
+import os
+import sys
+import types
+import itertools
+import struct
+import ctypes
+import collections
+import re
+import platform
from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
from cpython cimport PyErr_SetString
+#from cpython.string cimport PyString_FromStringAndSize, PyString_AS_STRING
+#from cpython.exc cimport PyErr_SetString, PyErr_NoMemory
+
# defines imported from samtools
DEF SEEK_SET = 0
DEF SEEK_CUR = 1
cdef int max_pos = 2 << 29
# redirect stderr to 0
-_logfile = open("/dev/null", "w")
+_logfile = open(os.path.devnull, "w")
pysam_set_stderr( PyFile_AsFile( _logfile ) )
#####################################################################
def __del__(self):
self.release()
+class StderrStoreWindows():
+ '''does nothing. stderr can't be redirected on windows'''
+ def __init__(self): pass
+ def readAndRelease(self): return []
+ def release(self): pass
+
+if platform.system()=='Windows':
+ del StderrStore
+ StderrStore = StderrStoreWindows
+
+
######################################################################
######################################################################
######################################################################
cdef class Samfile:
- '''*(filename, mode='r', template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
+ '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None)*
A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.
- *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode so for binary
+ *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary
(:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output.
- Use ``h`` to output header information in text (:term:`TAM`) mode.
+ Use ``h`` to output header information in text (:term:`TAM`) mode.
If ``b`` is present, it must immediately follow ``r`` or ``w``.
Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open
a :term:`BAM` formatted file for reading, type::
- import pysam
f = pysam.Samfile('ex1.bam','rb')
+ If mode is not specified, we will try to auto-detect in the order 'r', 'rb', thus both the following
+ should work::
+
+ f1 = pysam.Samfile('ex1.bam' )
+ f2 = pysam.Samfile('ex1.bam' )
+
If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random
access to reads via :meth:`fetch` and :meth:`pileup` is disabled.
'''
- cdef char * _filename
- # pointer to samfile
- cdef samfile_t * samfile
- # pointer to index
- cdef bam_index_t *index
- # true if file is a bam file
- cdef int isbam
- # true if file is not on the local filesystem
- cdef int isremote
- # current read within iteration
- cdef bam1_t * b
- # file opening mode
- cdef char * mode
-
def __cinit__(self, *args, **kwargs ):
self.samfile = NULL
self._filename = NULL
def _open( self,
char * filename,
- mode = 'r',
+ mode = None,
Samfile template = None,
referencenames = None,
referencelengths = None,
closed and a new file will be opened.
'''
+ # read mode autodetection
+ if mode is None:
+ try:
+ self._open(filename, 'r', template=template,
+ referencenames=referencenames,
+ referencelengths=referencelengths,
+ text=text, header=header, port=port)
+ return
+ except ValueError, msg:
+ pass
+ self._open(filename, 'rb', template=template,
+ referencenames=referencenames,
+ referencelengths=referencelengths,
+ text=text, header=header, port=port)
+ return
+
assert mode in ( "r","w","rb","wb", "wh", "wbu" ), "invalid file opening mode `%s`" % mode
assert filename != NULL
# try to detect errors
self.samfile = samopen( filename, mode, NULL )
if self.samfile == NULL:
- raise ValueError( "could not open file - is it SAM/BAM format?")
+ raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
if self.samfile.header == NULL:
- raise ValueError( "could not open file - is it SAM/BAM format?")
-
+ raise ValueError( "file does not have valid header (mode='%s') - is it SAM/BAM format?" % mode )
+
+ #disabled for autodetection to work
if self.samfile.header.n_targets == 0:
- raise ValueError( "could not open file - is it SAM/BAM format?")
+ raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
if self.samfile == NULL:
raise IOError("could not open file `%s`" % filename )
if self.index == NULL:
raise IOError("error while opening index `%s` " % filename )
+ def gettid( self, reference ):
+ '''
+ convert :term:`reference` name into numerical :term:`tid`
+
+ returns -1 if reference is not known.
+ '''
+ if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ return pysam_reference2tid( self.samfile.header, reference )
+
def getrname( self, tid ):
'''
convert numerical :term:`tid` into :term:`reference` name.'''
if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
if not 0 <= tid < self.samfile.header.n_targets:
- raise ValueError( "tid out of range 0<=tid<%i" % self.samfile.header.n_targets )
+ raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
return self.samfile.header.target_name[tid]
- def gettid( self, reference ):
- '''
- convert :term:`reference` name into numerical :term:`tid`
-
- returns -1 if reference is not known.
+ cdef char * _getrname( self, int tid ):
'''
+ convert numerical :term:`tid` into :term:`reference` name.'''
if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
- return pysam_reference2tid( self.samfile.header, reference )
+ if not 0 <= tid < self.samfile.header.n_targets:
+ raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
+ return self.samfile.header.target_name[tid]
def _parseRegion( self,
reference = None,
# implementing it all in pysam (makes use of khash).
cdef int rtid
- cdef int rstart
- cdef int rend
+ cdef long long rstart
+ cdef long long rend
rtid = -1
rstart = 0
rend = max_pos
- if start != None: rstart = start
- if end != None: rend = end
+ if start != None:
+ try:
+ rstart = start
+ except OverflowError:
+ raise ValueError( 'start out of range (%i)' % start )
+
+ if end != None:
+ try:
+ rend = end
+ except OverflowError:
+ raise ValueError( 'end out of range (%i)' % end )
if region:
parts = re.split( "[:-]", region )
not re-opened the file.
'''
- if not read.is_paired:
- raise ValueError( "read is unpaired" )
- if read.mate_is_unmapped:
- raise ValueError( "mate is unmapped" )
+ cdef uint32_t flag = read._delegate.core.flag
+
+ if flag & BAM_FPAIRED == 0:
+ raise ValueError( "read %s: is unpaired" % (read.qname))
+ if flag & BAM_FMUNMAP != 0:
+ raise ValueError( "mate %s: is unmapped" % (read.qname))
cdef MateData mate_data
mate_data.mate = NULL
# xor flags to get the other mate
cdef int x = BAM_FREAD1 + BAM_FREAD2
- mate_data.flag = ( read._delegate.core.flag ^ x) & x
+ mate_data.flag = ( flag ^ x) & x
bam_fetch(self.samfile.x.bam,
self.index,
else:
raise ValueError ("count for a region is not available for sam files" )
-
def pileup( self,
reference = None,
start = None,
*all* reads which overlap the region are returned. The first base returned will be the
first base of the first read *not* necessarily the first base of the region used in the query.
+ The maximum number of reads considered for pileup is *8000*. This limit is set by
+ :term:`csamtools`.
+
'''
cdef int rtid, rstart, rend, has_coord
cdef bam_plbuf_t *buf
bam_destroy1(self.b)
if self._filename != NULL: free( self._filename )
- def write( self, AlignedRead read ):
+ cpdef int write( self, AlignedRead read ) except -1:
'''
write a single :class:`pysam.AlignedRead` to disk.
returns the number of bytes written.
'''
if not self._isOpen():
- raise ValueError( "I/O operation on closed file" )
+ return 0
return samwrite( self.samfile, read._delegate )
x = {}
for field in fields[1:]:
key, value = field.split(":",1)
- if key not in VALID_HEADER_FIELDS[record]:
+ # uppercase keys must be valid
+ # lowercase are permitted for user fields
+ if key in VALID_HEADER_FIELDS[record]:
+ x[key] = VALID_HEADER_FIELDS[record][key](value)
+ elif not key.isupper():
+ x[key] = value
+ else:
raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
- x[key] = VALID_HEADER_FIELDS[record][key](value)
if VALID_HEADER_TYPES[record] == dict:
if record in result:
if record == "CO":
line.append( fields )
else:
+ # write fields of the specification
for key in VALID_HEADER_ORDER[record]:
if key in fields:
line.append( "%s:%s" % (key, str(fields[key])))
+ # write user fields
+ for key in fields:
+ if not key.isupper():
+ line.append( "%s:%s" % (key, str(fields[key])))
+
return "\t".join( line )
cdef bam_header_t * _buildHeader( self, new_header ):
iterate over mapped reads in a region.
- By default, the file is re-openend to avoid conflicts if
- multiple operators work on the same file. Set *reopen* = False
+ By default, the file is re-openend to avoid conflicts between
+ multiple iterators working on the same file. Set *reopen* = False
to not re-open *samfile*.
The samtools iterators assume that the file
cdef int retval
cdef Samfile samfile
cdef samfile_t * fp
+ # true if samfile belongs to this object
+ cdef int owns_samfile
def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ):
self.fp = samopen( samfile._filename, mode, NULL )
store.release()
assert self.fp != NULL
+ self.owns_samfile = True
+ else:
+ self.fp = self.samfile.samfile
+ self.owns_samfile = False
self.retval = 0
def __dealloc__(self):
bam_destroy1(self.b)
- samclose( self.fp )
+ if self.owns_samfile: samclose( self.fp )
cdef class IteratorRowAll(IteratorRow):
"""*(Samfile samfile, int reopen = True)*
iterate over all reads in *samfile*
- By default, the file is re-openend to avoid conflicts if
- multiple operators work on the same file. Set *reopen* = False
+ By default, the file is re-openend to avoid conflicts between
+ multiple iterators working on the same file. Set *reopen* = False
to not re-open *samfile*.
"""
cdef bam1_t * b
cdef samfile_t * fp
+ # true if samfile belongs to this object
+ cdef int owns_samfile
def __cinit__(self, Samfile samfile, int reopen = True ):
self.fp = samopen( samfile._filename, mode, NULL )
store.release()
assert self.fp != NULL
+ self.owns_samfile = True
+ else:
+ self.fp = samfile.samfile
+ self.owns_samfile = False
# allocate memory for alignment
self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
def __dealloc__(self):
bam_destroy1(self.b)
- samclose( self.fp )
-
+ if self.owns_samfile: samclose( self.fp )
cdef class IteratorRowAllRefs(IteratorRow):
"""iterates over all mapped reads by chaining iterators over each reference
else:
raise StopIteration
+cdef class IteratorRowSelection(IteratorRow):
+ """*(Samfile samfile)*
+
+ iterate over reads in *samfile* at a given list of file positions.
+ """
+
+ cdef bam1_t * b
+ cdef int current_pos
+ cdef samfile_t * fp
+ cdef positions
+ # true if samfile belongs to this object
+ cdef int owns_samfile
+
+ def __cinit__(self, Samfile samfile, positions, int reopen = True ):
+
+ if not samfile._isOpen():
+ raise ValueError( "I/O operation on closed file" )
+
+ if not samfile._isOpen():
+ raise ValueError( "I/O operation on closed file" )
+
+ assert samfile.isbam, "can only use this iterator on bam files"
+ mode = "rb"
+
+ # reopen the file to avoid iterator conflict
+ if reopen:
+ store = StderrStore()
+ self.fp = samopen( samfile._filename, mode, NULL )
+ store.release()
+ assert self.fp != NULL
+ self.owns_samfile = True
+ else:
+ self.fp = samfile.samfile
+ self.owns_samfile = False
+
+ # allocate memory for alignment
+ self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
+
+ self.positions = positions
+ self.current_pos = 0
+
+ def __iter__(self):
+ return self
+
+ cdef bam1_t * getCurrent( self ):
+ return self.b
+
+ cdef int cnext(self):
+ '''cversion of iterator'''
+
+ # end iteration if out of positions
+ if self.current_pos >= len(self.positions): return -1
+
+ bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
+ self.current_pos += 1
+ return samread(self.fp, self.b)
+
+ def __next__(self):
+ """python version of next().
+
+ pyrex uses this non-standard name instead of next()
+ """
+
+ cdef int ret = self.cnext()
+ if (ret > 0):
+ return makeAlignedRead( self.b )
+ else:
+ raise StopIteration
+
+ def __dealloc__(self):
+ bam_destroy1(self.b)
+ if self.owns_samfile: samclose( self.fp )
+
##-------------------------------------------------------------------
##-------------------------------------------------------------------
##-------------------------------------------------------------------
# reload sequence
if d.fastafile != NULL and b.core.tid != d.tid:
if d.seq != NULL: free(d.seq)
- d.tid = b.core.tid;
+ d.tid = b.core.tid
d.seq = faidx_fetch_seq(d.fastafile,
d.samfile.header.target_name[d.tid],
0, max_pos,
&d.seq_len)
-
if d.seq == NULL:
raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
(d.samfile.header.target_name[d.tid],
cdef class AlignedRead:
'''
- Class representing an aligned read. see SAM format specification for meaning of fields (http://samtools.sourceforge.net/).
+ Class representing an aligned read. see SAM format specification for
+ the meaning of fields (http://samtools.sourceforge.net/).
This class stores a handle to the samtools C-structure representing
an aligned read. Member read access is forwarded to the C-structure
be set *before* the quality scores. Setting the sequence will
also erase any quality scores that were set previously.
'''
- cdef:
- bam1_t * _delegate
# Now only called when instances are created from Python
def __init__(self):
bam_destroy1(self._delegate)
def __str__(self):
- """todo"""
+ """return string representation of alignment.
+
+ The representation is an approximate :term:`sam` format.
+
+ An aligned read might not be associated with a :term:`Samfile`.
+ As a result :term:`tid` is shown instead of the reference name.
+
+ Similarly, the tags field is returned in its parsed state.
+ """
+ # sam-parsing is done in sam.c/bam_format1_core which
+ # requires a valid header.
return "\t".join(map(str, (self.qname,
+ self.flag,
self.rname,
self.pos,
+ self.mapq,
self.cigar,
- self.qual,
- self.flag,
+ self.mrnm,
+ self.mpos,
+ self.rlen,
self.seq,
- self.mapq,
- self.tags)))
-
+ self.qual,
+ self.tags )))
def compare(self, AlignedRead other):
'''return -1,0,1, if contents in this are binary <,=,> to *other*'''
if val: self._delegate.core.flag |= BAM_FQCFAIL
else: self._delegate.core.flag &= ~BAM_FQCFAIL
property is_duplicate:
- """ true if optical or PCR duplicate"""
+ """true if optical or PCR duplicate"""
def __get__(self): return (self.flag & BAM_FDUP) != 0
def __set__(self,val):
if val: self._delegate.core.flag |= BAM_FDUP
else: self._delegate.core.flag &= ~BAM_FDUP
-
+ property positions:
+ """a list of reference positions that this read aligns to."""
+ def __get__(self):
+ cdef uint32_t k, i, pos
+ cdef int op
+ cdef uint32_t * cigar_p
+ cdef bam1_t * src
+
+ result = []
+ src = self._delegate
+ if src.core.n_cigar == 0: return []
+
+ pos = src.core.pos
+
+ cigar_p = bam1_cigar(src)
+ for k from 0 <= k < src.core.n_cigar:
+ op = cigar_p[k] & BAM_CIGAR_MASK
+ l = cigar_p[k] >> BAM_CIGAR_SHIFT
+ if op == BAM_CMATCH:
+ for i from pos <= i < pos + l:
+ result.append( i )
+
+ if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
+ pos += l
+
+ return result
+ def overlap( self, uint32_t start, uint32_t end ):
+ """return number of bases on reference overlapping *start* and *end*
+ """
+ cdef uint32_t k, i, pos, overlap
+ cdef int op, o
+ cdef uint32_t * cigar_p
+ cdef bam1_t * src
+
+ overlap = 0
+
+ src = self._delegate
+ if src.core.n_cigar == 0: return 0
+ pos = src.core.pos
+ o = 0
+
+ cigar_p = bam1_cigar(src)
+ for k from 0 <= k < src.core.n_cigar:
+ op = cigar_p[k] & BAM_CIGAR_MASK
+ l = cigar_p[k] >> BAM_CIGAR_SHIFT
+
+ if op == BAM_CMATCH:
+ o = min( pos + l, end) - max( pos, start )
+ if o > 0: overlap += o
+
+ if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
+ pos += l
+
+ return overlap
+
def opt(self, tag):
"""retrieves optional data given a two-letter *tag*"""
#see bam_aux.c: bam_aux_get() and bam_aux2i() etc
ofd = os.dup(self.id) # Save old stream on new unit.
self.streams.append(ofd)
sys.stdout.flush() # Buffered data goes to old stream.
+ sys.stderr.flush() # Buffered data goes to old stream.
os.dup2(fd, self.id) # Open unit 1 on new stream.
os.close(fd) # Close other unit (look out, caller.)
return self._call()
+
+
+cdef class IndexedReads:
+ """index a bamfile by read.
+
+ The index is kept in memory.
+
+ By default, the file is re-openend to avoid conflicts if
+ multiple operators work on the same file. Set *reopen* = False
+ to not re-open *samfile*.
+ """
+
+ cdef Samfile samfile
+ cdef samfile_t * fp
+ cdef index
+ # true if samfile belongs to this object
+ cdef int owns_samfile
+
+ def __init__(self, Samfile samfile, int reopen = True ):
+ self.samfile = samfile
+
+ if samfile.isbam: mode = "rb"
+ else: mode = "r"
+
+ # reopen the file - note that this makes the iterator
+ # slow and causes pileup to slow down significantly.
+ if reopen:
+ store = StderrStore()
+ self.fp = samopen( samfile._filename, mode, NULL )
+ store.release()
+ assert self.fp != NULL
+ self.owns_samfile = True
+ else:
+ self.fp = samfile.samfile
+ self.owns_samfile = False
+
+ assert samfile.isbam, "can only IndexReads on bam files"
+
+ def build( self ):
+ '''build index.'''
+
+ self.index = collections.defaultdict( list )
+
+ # this method will start indexing from the current file position
+ # if you decide
+ cdef int ret = 1
+ cdef bam1_t * b = <bam1_t*> calloc(1, sizeof( bam1_t) )
+
+ cdef uint64_t pos
+
+ while ret > 0:
+ pos = bam_tell( self.fp.x.bam )
+ ret = samread( self.fp, b)
+ if ret > 0:
+ qname = bam1_qname( b )
+ self.index[qname].append( pos )
+
+ bam_destroy1( b )
+
+ def find( self, qname ):
+ if qname in self.index:
+ return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
+ else:
+ raise KeyError( "read %s not found" % qname )
+
+ def __dealloc__(self):
+ if self.owns_samfile: samclose( self.fp )
+
__all__ = ["Samfile",
"Fastafile",
"IteratorRow",
"IteratorSNPCalls",
"SNPCaller",
"IndelCaller",
- "IteratorIndelCalls", ]
+ "IteratorIndelCalls",
+ "IndexedReads" ]
-/* Generated by Cython 0.13 on Fri Feb 11 09:01:45 2011 */
+/* Generated by Cython 0.13 on Thu May 5 14:57:46 2011 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#include "stdint.h"
#include "bgzf.h"
#include "tabix.h"
+#include "pythread.h"
/* inline attribute */
#ifndef CYTHON_INLINE
static const char *__pyx_f[] = {
"ctabix.pyx",
+ "bool.pxd",
+ "TabProxies.pxd",
};
/* Type declarations */
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":215
- * return str(v)
+/* "pysam/ctabix.pxd":178
+ * cdef tabix_t * tabixfile
+ *
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
+ */
+
+struct __pyx_obj_6ctabix_Parser {
+ PyObject_HEAD
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":293
+ * return r
+ *
+ * cdef class asVCF( Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a VCF record.'''
+ * def __call__(self, char * buffer, int len ):
+ */
+
+struct __pyx_obj_6ctabix_asVCF {
+ struct __pyx_obj_6ctabix_Parser __pyx_base;
+};
+
+/* "pysam/TabProxies.pxd":42
+ * ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
- * '''Proxy class for access to parsed row as a tuple.
*
+ * cdef:
*/
-struct __pyx_obj_6ctabix_TupleProxy {
+struct __pyx_obj_10TabProxies_TupleProxy {
PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_TupleProxy *__pyx_vtab;
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
char *data;
char **fields;
int nfields;
int index;
+ int nbytes;
+ int offset;
+ int is_modified;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":668
- * self.fromDict( r )
+/* "pysam/TabProxies.pxd":77
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class Parser: # <<<<<<<<<<<<<<
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_6ctabix_Parser {
- PyObject_HEAD
+struct __pyx_obj_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+};
+
+/* "pysam/TabProxies.pxd":80
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_obj_10TabProxies_BedProxy {
+ struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
+};
+
+/* "pysam/TabProxies.pxd":91
+ * 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;
+};
+
+/* "pysam/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 *contig;
+ char *source;
+ char *feature;
+ uint32_t start;
+ uint32_t end;
+ char *score;
+ char *strand;
+ char *frame;
+ char *attributes;
+ int hasOwnAttributes;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":156
- * return result
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":161
+ * return result
*
* cdef class TabixIterator: # <<<<<<<<<<<<<<
* """iterates over rows in *tabixfile* in region
tabix_t *tabixfile;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":689
- * return r
- *
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":304
+ * #########################################################
+ * #########################################################
* cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
* """iterates over mapped reads in a region.
- * """
+ *
*/
struct __pyx_obj_6ctabix_TabixIteratorParsed {
struct __pyx_obj_6ctabix_Parser *parser;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":6
- * import tempfile, os, sys, types, itertools, struct, ctypes
- *
- * cdef class Tabixfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode='r')*
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":216
+ * ti_iter_destroy(self.iterator)
*
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
+ * """return header lines.
+ * """
*/
-struct __pyx_obj_6ctabix_Tabixfile {
+struct __pyx_obj_6ctabix_TabixHeaderIterator {
PyObject_HEAD
- char *filename;
+ ti_iter_t iterator;
tabix_t *tabixfile;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":326
- * return self.fields[self.index-1]
+/* "pysam/ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
- * cdef class GTFProxy: # <<<<<<<<<<<<<<
- * '''Proxy class for access to GTF fields.
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ * cdef char * filename
*
*/
-struct __pyx_obj_6ctabix_GTFProxy {
+struct __pyx_obj_6ctabix_Tabixfile {
PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_GTFProxy *__pyx_vtab;
- char *contig;
- char *source;
- char *feature;
- uint32_t start;
- uint32_t end;
- char *score;
- char *strand;
- char *frame;
- char *attributes;
- int nbytes;
- char *data;
- int isModified;
- int hasOwnAttributes;
+ char *filename;
+ tabix_t *tabixfile;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":681
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":277
* return r
*
* cdef class asGTF(Parser): # <<<<<<<<<<<<<<
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":671
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":285
+ * return r
+ *
+ * cdef class asBed( Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a GTF record.'''
+ * def __call__(self, char * buffer, int len):
+ */
+
+struct __pyx_obj_6ctabix_asBed {
+ struct __pyx_obj_6ctabix_Parser __pyx_base;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":267
* pass
*
* cdef class asTuple(Parser): # <<<<<<<<<<<<<<
};
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":215
- * return str(v)
+/* "pysam/TabProxies.pxd":42
+ * ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
- * '''Proxy class for access to parsed row as a tuple.
*
+ * 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);
+};
+static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
+
+
+/* "pysam/TabProxies.pxd":77
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+
+
+/* "pysam/TabProxies.pxd":91
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+
+
+/* "pysam/TabProxies.pxd":80
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
*/
-struct __pyx_vtabstruct_6ctabix_TupleProxy {
- PyObject *(*take)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t);
- PyObject *(*present)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t);
- PyObject *(*copy)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t);
- PyObject *(*update)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t);
+struct __pyx_vtabstruct_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_6ctabix_TupleProxy *__pyx_vtabptr_6ctabix_TupleProxy;
+static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
-/* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":326
- * return self.fields[self.index-1]
+/* "pysam/TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class GTFProxy: # <<<<<<<<<<<<<<
- * '''Proxy class for access to GTF fields.
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_vtabstruct_6ctabix_GTFProxy {
- PyObject *(*take)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t);
- PyObject *(*present)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t);
- PyObject *(*copy)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t);
- PyObject *(*update)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t);
+struct __pyx_vtabstruct_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_6ctabix_GTFProxy *__pyx_vtabptr_6ctabix_GTFProxy;
+static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact); /*proto*/
-static CYTHON_INLINE long __Pyx_NegateNonNeg(long 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 double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
-
-#define __Pyx_PyObject_AsDouble(obj) \
- ((likely(PyFloat_CheckExact(obj))) ? \
- PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
-
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
-
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
-
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
-static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
+
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
static void __Pyx_AddTraceback(const char *funcname); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+/* Module declarations from cpython.version */
+
+/* Module declarations from cpython.ref */
+
+/* Module declarations from cpython.exc */
+
+/* Module declarations from cpython.module */
+
+/* Module declarations from cpython.mem */
+
+/* Module declarations from cpython.tuple */
+
+/* Module declarations from cpython.list */
+
+/* Module declarations from libc.stdio */
+
+/* Module declarations from cpython.object */
+
+/* Module declarations from cpython.sequence */
+
+/* Module declarations from cpython.mapping */
+
+/* Module declarations from cpython.iterator */
+
+/* Module declarations from cpython.type */
+
+/* Module declarations from cpython.number */
+
+/* Module declarations from cpython.int */
+
+/* Module declarations from __builtin__ */
+
+/* Module declarations from cpython.bool */
+
+static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0;
+/* Module declarations from cpython.long */
+
+/* Module declarations from cpython.float */
+
+/* Module declarations from cpython.complex */
+
+/* Module declarations from cpython.string */
+
+/* Module declarations from cpython.unicode */
+
+/* Module declarations from cpython.dict */
+
+/* Module declarations from cpython.instance */
+
+/* Module declarations from cpython.function */
+
+/* Module declarations from cpython.method */
+
+/* Module declarations from cpython.weakref */
+
+/* Module declarations from cpython.getargs */
+
+/* Module declarations from cpython.pythread */
+
+/* Module declarations from cpython.cobject */
+
+/* Module declarations from cpython.oldbuffer */
+
+/* Module declarations from cpython.set */
+
+/* Module declarations from cpython.buffer */
+
+/* Module declarations from cpython.bytes */
+
+/* Module declarations from cpython.pycapsule */
+
+/* Module declarations from cpython */
+
+/* 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 ctabix */
static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TupleProxy = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_GTFProxy = 0;
static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0;
+static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0;
+static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 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;
#define __Pyx_MODULE_NAME "ctabix"
int __pyx_module_is_main_ctabix = 0;
static PyObject *__pyx_builtin_IOError;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_StopIteration;
-static PyObject *__pyx_builtin_IndexError;
-static PyObject *__pyx_builtin_TypeError;
-static PyObject *__pyx_builtin_AttributeError;
static PyObject *__pyx_builtin_OSError;
static PyObject *__pyx_builtin_ord;
static PyObject *__pyx_builtin_KeyError;
static char __pyx_k_10[] = "end out of range (%i)";
static char __pyx_k_11[] = "I/O operation on closed file";
static char __pyx_k_12[] = "malformatted query or wrong sequence name.\n";
-static char __pyx_k_13[] = ".";
-static char __pyx_k_14[] = "\"%s\"";
-static char __pyx_k_15[] = "incomplete line at %s";
-static char __pyx_k_16[] = "row too large - more than %i fields";
-static char __pyx_k_17[] = "list index out of range";
-static char __pyx_k_18[] = "malformatted entry at %s";
-static char __pyx_k_19[] = ";";
-static char __pyx_k_20[] = " ";
-static char __pyx_k_21[] = "\"";
-static char __pyx_k_22[] = "%s \"%s\"";
-static char __pyx_k_23[] = "%s %s";
-static char __pyx_k_24[] = "; ";
-static char __pyx_k_25[] = "\t";
-static char __pyx_k_26[] = "";
-static char __pyx_k_27[] = "'GTFProxy' has no attribute '%s'";
-static char __pyx_k_29[] = "Filename '%s' already exists, use *force* to overwrite";
-static char __pyx_k_30[] = "could not open '%s' for writing";
-static char __pyx_k_31[] = "could not open '%s' for reading";
-static char __pyx_k_32[] = "writing failed";
-static char __pyx_k_34[] = "#";
-static char __pyx_k_36[] = "No such file '%s'";
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-static char __pyx_k_39[] = "unknown preset '%s', valid presets are '%s'";
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-static char __pyx_k_41[] = "chromosome names";
-static char __pyx_k_42[] = "contig of feature.";
-static char __pyx_k_43[] = "feature name.";
-static char __pyx_k_44[] = "feature source.";
-static char __pyx_k_45[] = "feature start (in 0-based open/closed coordinates).";
-static char __pyx_k_46[] = "feature end (in 0-based open/closed coordinates).";
-static char __pyx_k_47[] = "feature score.";
-static char __pyx_k_48[] = "feature strand.";
-static char __pyx_k_49[] = "feature frame.";
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-static char __pyx_k_59[] = "GTFProxy.asDict (line 521)";
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-static char __pyx_k_62[] = "GTFProxy.keys (line 616)";
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-static char __pyx_k_65[] = "TabixIteratorParsed.__next__ (line 725)";
-static char __pyx_k_66[] = "tabix_compress (line 741)";
-static char __pyx_k_67[] = "tabix_index (line 786)";
+static char __pyx_k_13[] = "can't open header.\n";
+static char __pyx_k_15[] = "Filename '%s' already exists, use *force* to overwrite";
+static char __pyx_k_16[] = "could not open '%s' for writing";
+static char __pyx_k_17[] = "could not open '%s' for reading";
+static char __pyx_k_18[] = "writing failed";
+static char __pyx_k_20[] = "#";
+static char __pyx_k_22[] = "No such file '%s'";
+static char __pyx_k_23[] = ".gz";
+static char __pyx_k_24[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
+static char __pyx_k_25[] = "unknown preset '%s', valid presets are '%s'";
+static char __pyx_k_26[] = ",";
+static char __pyx_k_27[] = "chromosome names";
+static char __pyx_k_28[] = "Tabixfile._isOpen (line 19)";
+static char __pyx_k_29[] = "Tabixfile._open (line 23)";
+static char __pyx_k_30[] = "Tabixfile._parseRegion (line 57)";
+static char __pyx_k_31[] = "Tabixfile.fetch (line 102)";
+static char __pyx_k_32[] = "Tabixfile.header.__get__ (line 140)";
+static char __pyx_k_33[] = "TabixIterator.__next__ (line 192)";
+static char __pyx_k_34[] = "TabixHeaderIterator.__next__ (line 239)";
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static char __pyx_k__r[] = "r";
static char __pyx_k__w[] = "w";
static char __pyx_k__bc[] = "bc";
static char __pyx_k__tid[] = "tid";
static char __pyx_k__vcf[] = "vcf";
static char __pyx_k__copy[] = "copy";
-static char __pyx_k__data[] = "data";
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static char __pyx_k__join[] = "join";
static char __pyx_k__keys[] = "keys";
static char __pyx_k__mode[] = "mode";
-static char __pyx_k__name[] = "name";
static char __pyx_k__path[] = "path";
static char __pyx_k___open[] = "_open";
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static char __pyx_k__asGTF[] = "asGTF";
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static char __pyx_k__close[] = "close";
static char __pyx_k__fetch[] = "fetch";
static char __pyx_k__force[] = "force";
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-static char __pyx_k__fields[] = "fields";
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-static char __pyx_k__nbytes[] = "nbytes";
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static char __pyx_k__parser[] = "parser";
static char __pyx_k__pileup[] = "pileup";
static char __pyx_k__preset[] = "preset";
static char __pyx_k__psltbl[] = "psltbl";
static char __pyx_k__region[] = "region";
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static char __pyx_k__IOError[] = "IOError";
static char __pyx_k__OSError[] = "OSError";
static char __pyx_k____all__[] = "__all__";
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static char __pyx_k___isOpen[] = "_isOpen";
static char __pyx_k__asTuple[] = "asTuple";
static char __pyx_k__end_col[] = "end_col";
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static char __pyx_k__seq_col[] = "seq_col";
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static char __pyx_k____main__[] = "__main__";
static char __pyx_k____test__[] = "__test__";
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static char __pyx_k__itertools[] = "itertools";
static char __pyx_k__line_skip[] = "line_skip";
static char __pyx_k__meta_char[] = "meta_char";
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static char __pyx_k__tabixfile[] = "tabixfile";
static char __pyx_k__zerobased[] = "zerobased";
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static char __pyx_k__ValueError[] = "ValueError";
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static char __pyx_k__tabix_index[] = "tabix_index";
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static char __pyx_k__filename_out[] = "filename_out";
-static char __pyx_k__setAttribute[] = "setAttribute";
static char __pyx_k__StopIteration[] = "StopIteration";
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-static char __pyx_k__AttributeError[] = "AttributeError";
static char __pyx_k__tabix_compress[] = "tabix_compress";
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static char __pyx_k__TabixIteratorParsed[] = "TabixIteratorParsed";
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static PyObject *__pyx_kp_s_10;
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static PyObject *__pyx_n_s__StopIteration;
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static PyObject *__pyx_n_s__TabixIterator;
static PyObject *__pyx_n_s__TabixIteratorParsed;
static PyObject *__pyx_n_s__Tabixfile;
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static PyObject *__pyx_n_s__ValueError;
static PyObject *__pyx_n_s____all__;
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static PyObject *__pyx_n_s__asGTF;
static PyObject *__pyx_n_s__asTuple;
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static PyObject *__pyx_n_s__bc;
static PyObject *__pyx_n_s__bed;
static PyObject *__pyx_n_s__buffer;
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static PyObject *__pyx_n_s__gff;
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static PyObject *__pyx_n_s__tabixfile;
static PyObject *__pyx_n_s__tempfile;
static PyObject *__pyx_n_s__tid;
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static PyObject *__pyx_int_0x10000;
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+ sizeof(struct __pyx_obj_6ctabix_Tabixfile), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_6ctabix_Tabixfile, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_Tabixfile, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Tabixfile, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Tabixfile, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_Tabixfile, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
+ __Pyx_DOCSTR("*(filename, mode='r')*\n\n opens a :term:`tabix file` for reading. A missing\n index (*filename* + \".tbi\") will raise an exception.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_6ctabix_Tabixfile, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_6ctabix_Tabixfile, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_6ctabix_Tabixfile, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- if (__pyx_pf_6ctabix_9Tabixfile___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_6ctabix_Parser(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_6ctabix_9Tabixfile_contigs(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_9Tabixfile_7contigs___get__(o);
-}
-
-static PyMethodDef __pyx_methods_6ctabix_Tabixfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_6ctabix_9Tabixfile__isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile__isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_6ctabix_9Tabixfile__open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile__open)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_6ctabix_9Tabixfile__parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile__parseRegion)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_6ctabix_9Tabixfile_fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_9Tabixfile_fetch)},
+static PyMethodDef __pyx_methods_6ctabix_Parser[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_6ctabix_Tabixfile[] = {
- {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_41), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_Tabixfile = {
+static PyNumberMethods __pyx_tp_as_number_Parser = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_Tabixfile = {
+static PySequenceMethods __pyx_tp_as_sequence_Parser = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_Tabixfile = {
+static PyMappingMethods __pyx_tp_as_mapping_Parser = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_Tabixfile = {
+static PyBufferProcs __pyx_tp_as_buffer_Parser = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_6ctabix_Tabixfile = {
+PyTypeObject __pyx_type_6ctabix_Parser = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.Tabixfile"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_Tabixfile), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.Parser"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_Parser), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Tabixfile, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_Tabixfile, /*tp_as_number*/
- &__pyx_tp_as_sequence_Tabixfile, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Tabixfile, /*tp_as_mapping*/
+ &__pyx_tp_as_number_Parser, /*tp_as_number*/
+ &__pyx_tp_as_sequence_Parser, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_Parser, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Tabixfile, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_Parser, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("*(filename, mode='r')*\n\n opens a :term:`tabix file` for reading. A missing\n index (*filename* + \".tbi\") will raise an exception.\n "), /*tp_doc*/
+ 0, /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_Tabixfile, /*tp_methods*/
+ __pyx_methods_6ctabix_Parser, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_6ctabix_Tabixfile, /*tp_getset*/
+ 0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_Tabixfile, /*tp_new*/
+ __pyx_tp_new_6ctabix_Parser, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_6ctabix_TupleProxy __pyx_vtable_6ctabix_TupleProxy;
-static PyObject *__pyx_tp_new_6ctabix_TupleProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_6ctabix_TupleProxy *p;
+static PyObject *__pyx_tp_new_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_6ctabix_TupleProxy *)o);
- p->__pyx_vtab = __pyx_vtabptr_6ctabix_TupleProxy;
- if (__pyx_pf_6ctabix_10TupleProxy___cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ if (__pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_TupleProxy(PyObject *o) {
+static void __pyx_tp_dealloc_6ctabix_TabixHeaderIterator(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_6ctabix_10TupleProxy___dealloc__(o);
+ __pyx_pf_6ctabix_19TabixHeaderIterator___dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_sq_item_6ctabix_TupleProxy(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);
- Py_DECREF(x);
- return r;
-}
-static PyMethodDef __pyx_methods_6ctabix_TupleProxy[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_6ctabix_10TupleProxy___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_10TupleProxy___next__)},
+static PyMethodDef __pyx_methods_6ctabix_TabixHeaderIterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_6ctabix_19TabixHeaderIterator___next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixHeaderIterator___next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_TupleProxy = {
+static PyNumberMethods __pyx_tp_as_number_TabixHeaderIterator = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_TupleProxy = {
- __pyx_pf_6ctabix_10TupleProxy___len__, /*sq_length*/
+static PySequenceMethods __pyx_tp_as_sequence_TabixHeaderIterator = {
+ 0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
- __pyx_sq_item_6ctabix_TupleProxy, /*sq_item*/
+ 0, /*sq_item*/
0, /*sq_slice*/
0, /*sq_ass_item*/
0, /*sq_ass_slice*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_TupleProxy = {
- __pyx_pf_6ctabix_10TupleProxy___len__, /*mp_length*/
- __pyx_pf_6ctabix_10TupleProxy___getitem__, /*mp_subscript*/
+static PyMappingMethods __pyx_tp_as_mapping_TabixHeaderIterator = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_TupleProxy = {
+static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_6ctabix_TupleProxy = {
+PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.TupleProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_TupleProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.TabixHeaderIterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_TupleProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_TabixHeaderIterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_TupleProxy, /*tp_as_number*/
- &__pyx_tp_as_sequence_TupleProxy, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TupleProxy, /*tp_as_mapping*/
+ &__pyx_tp_as_number_TabixHeaderIterator, /*tp_as_number*/
+ &__pyx_tp_as_sequence_TabixHeaderIterator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_TabixHeaderIterator, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_TupleProxy, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_TabixHeaderIterator, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("Proxy class for access to parsed row as a tuple.\n\n This class represents a table row for fast read-access.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_6ctabix_10TupleProxy___iter__, /*tp_iter*/
- __pyx_pf_6ctabix_10TupleProxy___next__, /*tp_iternext*/
- __pyx_methods_6ctabix_TupleProxy, /*tp_methods*/
+ __pyx_pf_6ctabix_19TabixHeaderIterator___iter__, /*tp_iter*/
+ __pyx_pf_6ctabix_19TabixHeaderIterator___next__, /*tp_iternext*/
+ __pyx_methods_6ctabix_TabixHeaderIterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_TupleProxy, /*tp_new*/
+ __pyx_tp_new_6ctabix_TabixHeaderIterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_6ctabix_GTFProxy __pyx_vtable_6ctabix_GTFProxy;
-
-static PyObject *__pyx_tp_new_6ctabix_GTFProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_6ctabix_GTFProxy *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_obj_6ctabix_GTFProxy *)o);
- p->__pyx_vtab = __pyx_vtabptr_6ctabix_GTFProxy;
- if (__pyx_pf_6ctabix_8GTFProxy___cinit__(o, __pyx_empty_tuple, NULL) < 0) {
- Py_DECREF(o); o = 0;
- }
- return o;
-}
-
-static void __pyx_tp_dealloc_6ctabix_GTFProxy(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_6ctabix_8GTFProxy___dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- (*Py_TYPE(o)->tp_free)(o);
-}
-static PyObject *__pyx_sq_item_6ctabix_GTFProxy(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);
- Py_DECREF(x);
- return r;
-}
-static PyObject *__pyx_tp_getattro_6ctabix_GTFProxy(PyObject *o, PyObject *n) {
- PyObject *v = PyObject_GenericGetAttr(o, n);
- if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Clear();
- v = __pyx_pf_6ctabix_8GTFProxy___getattr__(o, n);
- }
- return v;
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_contig(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_6contig___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_contig(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_6contig___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_feature(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_7feature___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_feature(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_7feature___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_source(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_6source___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_source(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_6source___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_start(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_5start___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_start(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_5start___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_end(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_3end___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_end(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_3end___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_score(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_5score___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_score(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_5score___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_strand(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_6strand___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_strand(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_6strand___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_frame(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_5frame___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_frame(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_5frame___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
-}
-
-static PyObject *__pyx_getprop_6ctabix_8GTFProxy_attributes(PyObject *o, void *x) {
- return __pyx_pf_6ctabix_8GTFProxy_10attributes___get__(o);
-}
-
-static int __pyx_setprop_6ctabix_8GTFProxy_attributes(PyObject *o, PyObject *v, void *x) {
- if (v) {
- return __pyx_pf_6ctabix_8GTFProxy_10attributes___set__(o, v);
- }
- else {
- PyErr_SetString(PyExc_NotImplementedError, "__del__");
- return -1;
- }
+static PyObject *__pyx_tp_new_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
+ if (!o) return 0;
+ return o;
}
-static PyMethodDef __pyx_methods_6ctabix_GTFProxy[] = {
- {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pf_6ctabix_8GTFProxy_asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_6ctabix_8GTFProxy_asDict)},
- {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pf_6ctabix_8GTFProxy_fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_6ctabix_8GTFProxy_fromDict)},
- {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pf_6ctabix_8GTFProxy_invert, METH_O, __Pyx_DOCSTR(__pyx_doc_6ctabix_8GTFProxy_invert)},
- {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pf_6ctabix_8GTFProxy_keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_6ctabix_8GTFProxy_keys)},
- {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pf_6ctabix_8GTFProxy___getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_8GTFProxy___getattr__)},
- {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pf_6ctabix_8GTFProxy_setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_8GTFProxy_setAttribute)},
+static PyMethodDef __pyx_methods_6ctabix_asTuple[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_6ctabix_GTFProxy[] = {
- {(char *)"contig", __pyx_getprop_6ctabix_8GTFProxy_contig, __pyx_setprop_6ctabix_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_42), 0},
- {(char *)"feature", __pyx_getprop_6ctabix_8GTFProxy_feature, __pyx_setprop_6ctabix_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_43), 0},
- {(char *)"source", __pyx_getprop_6ctabix_8GTFProxy_source, __pyx_setprop_6ctabix_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_44), 0},
- {(char *)"start", __pyx_getprop_6ctabix_8GTFProxy_start, __pyx_setprop_6ctabix_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_45), 0},
- {(char *)"end", __pyx_getprop_6ctabix_8GTFProxy_end, __pyx_setprop_6ctabix_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_46), 0},
- {(char *)"score", __pyx_getprop_6ctabix_8GTFProxy_score, __pyx_setprop_6ctabix_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_47), 0},
- {(char *)"strand", __pyx_getprop_6ctabix_8GTFProxy_strand, __pyx_setprop_6ctabix_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_48), 0},
- {(char *)"frame", __pyx_getprop_6ctabix_8GTFProxy_frame, __pyx_setprop_6ctabix_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_49), 0},
- {(char *)"attributes", __pyx_getprop_6ctabix_8GTFProxy_attributes, __pyx_setprop_6ctabix_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_50), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_GTFProxy = {
+static PyNumberMethods __pyx_tp_as_number_asTuple = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_GTFProxy = {
+static PySequenceMethods __pyx_tp_as_sequence_asTuple = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
- __pyx_sq_item_6ctabix_GTFProxy, /*sq_item*/
+ 0, /*sq_item*/
0, /*sq_slice*/
0, /*sq_ass_item*/
0, /*sq_ass_slice*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_GTFProxy = {
+static PyMappingMethods __pyx_tp_as_mapping_asTuple = {
0, /*mp_length*/
- __pyx_pf_6ctabix_8GTFProxy___getitem__, /*mp_subscript*/
+ 0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_GTFProxy = {
+static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_6ctabix_GTFProxy = {
+PyTypeObject __pyx_type_6ctabix_asTuple = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.GTFProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_GTFProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asTuple"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asTuple), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_GTFProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_GTFProxy, /*tp_as_number*/
- &__pyx_tp_as_sequence_GTFProxy, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_GTFProxy, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asTuple, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/
0, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pf_6ctabix_8GTFProxy___str__, /*tp_str*/
- __pyx_tp_getattro_6ctabix_GTFProxy, /*tp_getattro*/
+ __pyx_pf_6ctabix_7asTuple___call__, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_GTFProxy, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("Proxy class for access to GTF fields.\n\n This class represents a GTF entry for fast read-access.\n Write-access has been added as well, though some care must\n be taken. If any of the string fields (contig, source, ...)\n are set, the new value is tied to the lifetime of the\n argument that was supplied.\n\n The only exception is the attributes field when set from\n a dictionary - this field will manage its own memory.\n\n "), /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_GTFProxy, /*tp_methods*/
+ __pyx_methods_6ctabix_asTuple, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_6ctabix_GTFProxy, /*tp_getset*/
+ 0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_GTFProxy, /*tp_new*/
+ __pyx_tp_new_6ctabix_asTuple, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_6ctabix_Parser(PyObject *o) {
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static PyMethodDef __pyx_methods_6ctabix_Parser[] = {
+static PyMethodDef __pyx_methods_6ctabix_asGTF[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_Parser = {
+static PyNumberMethods __pyx_tp_as_number_asGTF = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_Parser = {
+static PySequenceMethods __pyx_tp_as_sequence_asGTF = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_Parser = {
+static PyMappingMethods __pyx_tp_as_mapping_asGTF = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_Parser = {
+static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_6ctabix_Parser = {
+PyTypeObject __pyx_type_6ctabix_asGTF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.Parser"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_Parser), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asGTF"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asGTF), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_Parser, /*tp_as_number*/
- &__pyx_tp_as_sequence_Parser, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_Parser, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asGTF, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/
0, /*tp_hash*/
- 0, /*tp_call*/
+ __pyx_pf_6ctabix_5asGTF___call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_Parser, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- 0, /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_Parser, /*tp_methods*/
+ __pyx_methods_6ctabix_asGTF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_Parser, /*tp_new*/
+ __pyx_tp_new_6ctabix_asGTF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asTuple[] = {
+static PyMethodDef __pyx_methods_6ctabix_asBed[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asTuple = {
+static PyNumberMethods __pyx_tp_as_number_asBed = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asTuple = {
+static PySequenceMethods __pyx_tp_as_sequence_asBed = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asTuple = {
+static PyMappingMethods __pyx_tp_as_mapping_asBed = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
+static PyBufferProcs __pyx_tp_as_buffer_asBed = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_6ctabix_asTuple = {
+PyTypeObject __pyx_type_6ctabix_asBed = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asTuple"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asTuple), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asBed"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asBed), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asTuple, /*tp_as_number*/
- &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asBed, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pf_6ctabix_7asTuple___call__, /*tp_call*/
+ __pyx_pf_6ctabix_5asBed___call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asBed, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple."), /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asTuple, /*tp_methods*/
+ __pyx_methods_6ctabix_asBed, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asTuple, /*tp_new*/
+ __pyx_tp_new_6ctabix_asBed, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asGTF[] = {
+static PyMethodDef __pyx_methods_6ctabix_asVCF[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_asGTF = {
+static PyNumberMethods __pyx_tp_as_number_asVCF = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_asGTF = {
+static PySequenceMethods __pyx_tp_as_sequence_asVCF = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_asGTF = {
+static PyMappingMethods __pyx_tp_as_mapping_asVCF = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
+static PyBufferProcs __pyx_tp_as_buffer_asVCF = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
#endif
};
-PyTypeObject __pyx_type_6ctabix_asGTF = {
+PyTypeObject __pyx_type_6ctabix_asVCF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asGTF"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asGTF), /*tp_basicsize*/
+ __Pyx_NAMESTR("ctabix.asVCF"), /*tp_name*/
+ sizeof(struct __pyx_obj_6ctabix_asVCF), /*tp_basicsize*/
0, /*tp_itemsize*/
__pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_asGTF, /*tp_as_number*/
- &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/
+ &__pyx_tp_as_number_asVCF, /*tp_as_number*/
+ &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pf_6ctabix_5asGTF___call__, /*tp_call*/
+ __pyx_pf_6ctabix_5asVCF___call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_asVCF, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER, /*tp_flags*/
- __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record."), /*tp_doc*/
+ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asGTF, /*tp_methods*/
+ __pyx_methods_6ctabix_asVCF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asGTF, /*tp_new*/
+ __pyx_tp_new_6ctabix_asVCF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_TabixIteratorParsed, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over mapped reads in a region.\n "), /*tp_doc*/
+ __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*/
0, /*tp_richcompare*/
};
static PyMethodDef __pyx_methods[] = {
- {__Pyx_NAMESTR("toDot"), (PyCFunction)__pyx_pf_6ctabix_toDot, METH_O, __Pyx_DOCSTR(__pyx_doc_6ctabix_toDot)},
- {__Pyx_NAMESTR("quote"), (PyCFunction)__pyx_pf_6ctabix_quote, METH_O, __Pyx_DOCSTR(__pyx_doc_6ctabix_quote)},
{__Pyx_NAMESTR("tabix_compress"), (PyCFunction)__pyx_pf_6ctabix_tabix_compress, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_tabix_compress)},
{__Pyx_NAMESTR("tabix_index"), (PyCFunction)__pyx_pf_6ctabix_tabix_index, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_6ctabix_tabix_index)},
{0, 0, 0, 0}
{&__pyx_kp_s_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 0, 1, 0},
{&__pyx_kp_s_12, __pyx_k_12, sizeof(__pyx_k_12), 0, 0, 1, 0},
{&__pyx_kp_s_13, __pyx_k_13, sizeof(__pyx_k_13), 0, 0, 1, 0},
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{&__pyx_kp_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 0},
{&__pyx_kp_s_16, __pyx_k_16, sizeof(__pyx_k_16), 0, 0, 1, 0},
{&__pyx_kp_s_17, __pyx_k_17, sizeof(__pyx_k_17), 0, 0, 1, 0},
{&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
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{&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
{&__pyx_kp_s_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 1, 0},
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{&__pyx_kp_s_22, __pyx_k_22, sizeof(__pyx_k_22), 0, 0, 1, 0},
{&__pyx_kp_s_23, __pyx_k_23, sizeof(__pyx_k_23), 0, 0, 1, 0},
{&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
{&__pyx_kp_s_25, __pyx_k_25, sizeof(__pyx_k_25), 0, 0, 1, 0},
{&__pyx_kp_s_26, __pyx_k_26, sizeof(__pyx_k_26), 0, 0, 1, 0},
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- {&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
+ {&__pyx_kp_u_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 1, 0, 0},
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{&__pyx_kp_s_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 0, 1, 0},
- {&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
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- {&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
- {&__pyx_kp_s_34, __pyx_k_34, sizeof(__pyx_k_34), 0, 0, 1, 0},
- {&__pyx_kp_s_36, __pyx_k_36, sizeof(__pyx_k_36), 0, 0, 1, 0},
- {&__pyx_kp_s_37, __pyx_k_37, sizeof(__pyx_k_37), 0, 0, 1, 0},
- {&__pyx_kp_s_38, __pyx_k_38, sizeof(__pyx_k_38), 0, 0, 1, 0},
- {&__pyx_kp_s_39, __pyx_k_39, sizeof(__pyx_k_39), 0, 0, 1, 0},
+ {&__pyx_kp_u_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 1, 0, 0},
+ {&__pyx_kp_u_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 1, 0, 0},
+ {&__pyx_kp_u_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 1, 0, 0},
+ {&__pyx_kp_u_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 1, 0, 0},
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+ if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_TabixIterator = &__pyx_type_6ctabix_TabixIterator;
- __pyx_vtabptr_6ctabix_TupleProxy = &__pyx_vtable_6ctabix_TupleProxy;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_6ctabix_TupleProxy.take = (PyObject *(*)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t))__pyx_f_6ctabix_10TupleProxy_take;
- __pyx_vtable_6ctabix_TupleProxy.present = (PyObject *(*)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t))__pyx_f_6ctabix_10TupleProxy_present;
- __pyx_vtable_6ctabix_TupleProxy.copy = (PyObject *(*)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t))__pyx_f_6ctabix_10TupleProxy_copy;
- __pyx_vtable_6ctabix_TupleProxy.update = (PyObject *(*)(struct __pyx_obj_6ctabix_TupleProxy *, char *, size_t))__pyx_f_6ctabix_10TupleProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_6ctabix_TupleProxy.take = (void(*)(void))__pyx_f_6ctabix_10TupleProxy_take;
- *(void(**)(void))&__pyx_vtable_6ctabix_TupleProxy.present = (void(*)(void))__pyx_f_6ctabix_10TupleProxy_present;
- *(void(**)(void))&__pyx_vtable_6ctabix_TupleProxy.copy = (void(*)(void))__pyx_f_6ctabix_10TupleProxy_copy;
- *(void(**)(void))&__pyx_vtable_6ctabix_TupleProxy.update = (void(*)(void))__pyx_f_6ctabix_10TupleProxy_update;
- #endif
- if (PyType_Ready(&__pyx_type_6ctabix_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- {
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TupleProxy, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_6ctabix_10TupleProxy___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_6ctabix_10TupleProxy___next__.doc = __pyx_doc_6ctabix_10TupleProxy___next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_10TupleProxy___next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_6ctabix_TupleProxy.tp_dict, __pyx_vtabptr_6ctabix_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "TupleProxy", (PyObject *)&__pyx_type_6ctabix_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_TupleProxy = &__pyx_type_6ctabix_TupleProxy;
- __pyx_vtabptr_6ctabix_GTFProxy = &__pyx_vtable_6ctabix_GTFProxy;
- #if PY_MAJOR_VERSION >= 3
- __pyx_vtable_6ctabix_GTFProxy.take = (PyObject *(*)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t))__pyx_f_6ctabix_8GTFProxy_take;
- __pyx_vtable_6ctabix_GTFProxy.present = (PyObject *(*)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t))__pyx_f_6ctabix_8GTFProxy_present;
- __pyx_vtable_6ctabix_GTFProxy.copy = (PyObject *(*)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t))__pyx_f_6ctabix_8GTFProxy_copy;
- __pyx_vtable_6ctabix_GTFProxy.update = (PyObject *(*)(struct __pyx_obj_6ctabix_GTFProxy *, char *, size_t))__pyx_f_6ctabix_8GTFProxy_update;
- #else
- *(void(**)(void))&__pyx_vtable_6ctabix_GTFProxy.take = (void(*)(void))__pyx_f_6ctabix_8GTFProxy_take;
- *(void(**)(void))&__pyx_vtable_6ctabix_GTFProxy.present = (void(*)(void))__pyx_f_6ctabix_8GTFProxy_present;
- *(void(**)(void))&__pyx_vtable_6ctabix_GTFProxy.copy = (void(*)(void))__pyx_f_6ctabix_8GTFProxy_copy;
- *(void(**)(void))&__pyx_vtable_6ctabix_GTFProxy.update = (void(*)(void))__pyx_f_6ctabix_8GTFProxy_update;
- #endif
- if (PyType_Ready(&__pyx_type_6ctabix_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_6ctabix_8GTFProxy___getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_6ctabix_8GTFProxy___getattr__.doc = __pyx_doc_6ctabix_8GTFProxy___getattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_8GTFProxy___getattr__;
+ __pyx_wrapperbase_6ctabix_19TabixHeaderIterator___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_6ctabix_19TabixHeaderIterator___next__.doc = __pyx_doc_6ctabix_19TabixHeaderIterator___next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixHeaderIterator___next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_6ctabix_GTFProxy.tp_dict, __pyx_vtabptr_6ctabix_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_6ctabix_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_GTFProxy = &__pyx_type_6ctabix_GTFProxy;
- if (PyType_Ready(&__pyx_type_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 668; __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 = 668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_Parser = &__pyx_type_6ctabix_Parser;
+ if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_6ctabix_TabixHeaderIterator = &__pyx_type_6ctabix_TabixHeaderIterator;
__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 = 671; __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 = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_asTuple) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 267; __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 = 267; __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 = 681; __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 = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 277; __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 = 277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_asGTF = &__pyx_type_6ctabix_asGTF;
- if (PyType_Ready(&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __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 = 285; __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 = 285; __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 = 293; __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 = 293; __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 = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__pyx_wrapperbase_6ctabix_19TabixIteratorParsed___next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
__pyx_wrapperbase_6ctabix_19TabixIteratorParsed___next__.doc = __pyx_doc_6ctabix_19TabixIteratorParsed___next__;
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixIteratorParsed___next__;
}
}
- if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_TabixIteratorParsed = &__pyx_type_6ctabix_TabixIteratorParsed;
/*--- Type import code ---*/
+ __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[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __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[2]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_GetVtable(__pyx_ptype_10TabProxies_TupleProxy->tp_dict, &__pyx_vtabptr_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 42; __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;}
+ if (__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict, &__pyx_vtabptr_10TabProxies_GTFProxy) < 0) {__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 = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict, &__pyx_vtabptr_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict, &__pyx_vtabptr_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict, &__pyx_vtabptr_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":4
+ /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":4
* # adds doc-strings for sphinx
*
- * import tempfile, os, sys, types, itertools, struct, ctypes # <<<<<<<<<<<<<<
- *
- * cdef class Tabixfile:
+ * import tempfile, os, sys, types, itertools, struct, ctypes, gzip # <<<<<<<<<<<<<<
+ * from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
+ * cimport TabProxies
*/
__pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__tempfile), 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_1);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__ctypes, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__gzip, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":743
+ /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":364
* def tabix_compress( filename_in,
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* force = False ): # <<<<<<<<<<<<<<
*
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*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_k_28 = __pyx_t_1;
+ __pyx_k_14 = __pyx_t_1;
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":787
+ /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":408
*
* def tabix_index( filename,
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- __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_k_33 = __pyx_t_1;
+ __pyx_k_19 = __pyx_t_1;
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":793
+ /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":414
* preset = None,
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+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); 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_k_35 = __pyx_t_1;
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__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- /* "/net/cpp-compute/backup/andreas/projects/pysam/pysam/pysam/ctabix.pyx":876
+ /* "/ifs/devel/pysam/pysam/pysam/ctabix.pyx":497
* return filename
*
* __all__ = ["tabix_index", # <<<<<<<<<<<<<<
* "tabix_compress",
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- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__setAttribute); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_35), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_64), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__TabixIteratorParsed); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s____next__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_compress); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_65), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_36), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_compress); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_index); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = __Pyx_GetAttrString(__pyx_t_2, "__doc__"); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_66), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_m, __pyx_n_s__tabix_index); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = __Pyx_GetAttrString(__pyx_t_3, "__doc__"); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_37), __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_kp_u_67), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/ctabix.pxd":2
+ /* "/ifs/apps/apps/python-2.7.1/lib/python2.7/site-packages/Cython-0.13-py2.7-linux-x86_64.egg/Cython/Includes/cpython/type.pxd":2
+ *
+ * cdef extern from "Python.h": # <<<<<<<<<<<<<<
+ * # The C structure of the objects used to describe built-in types.
*
- * cdef extern from "string.h": # <<<<<<<<<<<<<<
- * ctypedef int size_t
- * void *memcpy(void *dst,void *src,size_t len)
*/
goto __pyx_L0;
__pyx_L1_error:;
return 0;
}
-static double __Pyx__PyObject_AsDouble(PyObject* obj) {
- PyObject* float_value;
- 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)) {
-#if PY_MAJOR_VERSION >= 3
- float_value = PyFloat_FromString(obj);
-#else
- float_value = PyFloat_FromString(obj, 0);
-#endif
- } else {
- PyObject* args = PyTuple_New(1);
- if (unlikely(!args)) goto bad;
- PyTuple_SET_ITEM(args, 0, obj);
- float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0);
- PyTuple_SET_ITEM(args, 0, 0);
- Py_DECREF(args);
- }
- if (likely(float_value)) {
- double value = PyFloat_AS_DOUBLE(float_value);
- Py_DECREF(float_value);
- return value;
- }
-bad:
- return (double)-1;
-}
-
static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
}
}
#endif
-static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
- const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if ((sizeof(uint32_t) == sizeof(char)) ||
- (sizeof(uint32_t) == sizeof(short))) {
- return PyInt_FromLong((long)val);
- } else if ((sizeof(uint32_t) == sizeof(int)) ||
- (sizeof(uint32_t) == sizeof(long))) {
- if (is_unsigned)
- return PyLong_FromUnsignedLong((unsigned long)val);
- else
- return PyInt_FromLong((long)val);
- } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
- else
- return PyLong_FromLongLong((PY_LONG_LONG)val);
- } else {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
- const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint32_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint32_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint32_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint32_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- uint32_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (uint32_t)-1;
- }
-}
-
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;
}
}
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#ifndef __PYX_HAVE_RT_ImportType
+#define __PYX_HAVE_RT_ImportType
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
+ long size, int strict)
+{
+ PyObject *py_module = 0;
+ PyObject *result = 0;
+ PyObject *py_name = 0;
+ char warning[200];
+
+ py_module = __Pyx_ImportModule(module_name);
+ if (!py_module)
+ goto bad;
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(class_name);
+ #else
+ py_name = PyUnicode_FromString(class_name);
+ #endif
+ if (!py_name)
+ goto bad;
+ result = PyObject_GetAttr(py_module, py_name);
+ Py_DECREF(py_name);
+ py_name = 0;
+ Py_DECREF(py_module);
+ py_module = 0;
+ if (!result)
+ goto bad;
+ if (!PyType_Check(result)) {
+ PyErr_Format(PyExc_TypeError,
+ "%s.%s is not a type object",
+ module_name, class_name);
+ goto bad;
+ }
+ if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
+ PyOS_snprintf(warning, sizeof(warning),
+ "%s.%s size changed, may indicate binary incompatibility",
+ module_name, class_name);
+ #if PY_VERSION_HEX < 0x02050000
+ PyErr_Warn(NULL, warning);
+ #else
+ PyErr_WarnEx(NULL, warning, 0);
+ #endif
+ }
+ else if (((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%s.%s has the wrong size, try recompiling",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_module);
+ Py_XDECREF(result);
+ return 0;
+}
+#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;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ 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 int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
+ PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
if (!ob)
goto bad;
- if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
+#else
+ *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
+#endif
+ if (!*(void **)vtabptr)
goto bad;
Py_DECREF(ob);
return 0;
# tabix support
cdef extern from "tabix.h":
- ctypedef struct ti_index_t:
- pass
+ ctypedef struct ti_conf_t:
+ int32_t preset
+ int32_t sc, bc, ec
+ int32_t meta_char, line_skip
+ ctypedef struct ti_index_t:
+ pass
+
ctypedef struct tabix_t:
BGZF *fp
ti_index_t *idx
ctypedef struct ti_iter_t:
pass
- ctypedef struct ti_conf_t:
- int32_t preset
- int32_t sc, bc, ec
- int32_t meta_char, line_skip
-
tabix_t *ti_open(char *fn, char *fnidx)
int ti_lazy_index_load(tabix_t *t)
# pointer should be freed by a single free() call by the routine
# calling this function. The number of sequences is returned at *n
char **ti_seqname(ti_index_t *idx, int *n)
-
# Destroy the iterator
void ti_iter_destroy(ti_iter_t iter)
# /* Get the data line pointed by the iterator and iterate to the next record. */
# char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+
+cdef class Tabixfile:
+ cdef char * filename
+
+ # pointer to tabixfile
+ cdef tabix_t * tabixfile
+
+cdef class Parser:
+ pass
# cython: embedsignature=True
# adds doc-strings for sphinx
-import tempfile, os, sys, types, itertools, struct, ctypes
+import tempfile, os, sys, types, itertools, struct, ctypes, gzip
+from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
+cimport TabProxies
cdef class Tabixfile:
'''*(filename, mode='r')*
index (*filename* + ".tbi") will raise an exception.
'''
- cdef char * filename
-
- # pointer to tabixfile
- cdef tabix_t * tabixfile
-
def __cinit__(self, *args, **kwargs ):
self.tabixfile = NULL
self._open( *args, **kwargs )
else:
return TabixIteratorParsed( self, -1, 0, 0, parser )
+ property header:
+ def __get__( self ):
+ '''return header lines as an iterator.
+
+ Note that the header lines do not contain the newline '\n' character.
+ '''
+ return TabixHeaderIterator( self )
+
property contigs:
- '''chromosome names'''
- def __get__(self):
- cdef char ** sequences
- cdef int nsequences
+ '''chromosome names'''
+ def __get__(self):
+ cdef char ** sequences
+ cdef int nsequences
- ti_lazy_index_load( self.tabixfile )
- sequences = ti_seqname( self.tabixfile.idx, &nsequences )
- cdef int x
- result = []
- for x from 0 <= x < nsequences:
- result.append( sequences[x] )
- return result
+ ti_lazy_index_load( self.tabixfile )
+ sequences = ti_seqname( self.tabixfile.idx, &nsequences )
+ cdef int x
+ result = []
+ for x from 0 <= x < nsequences:
+ result.append( sequences[x] )
+ return result
cdef class TabixIterator:
"""iterates over rows in *tabixfile* in region
cdef char * s
cdef int len
- s = ti_read(self.tabixfile, self.iterator, &len)
- if s == NULL: raise StopIteration
+ # metachar filtering does not work within tabix
+ # though it should. Getting the metachar is a pain
+ # as ti_index_t is incomplete type.
+
+ # simply use '#' for now.
+ while 1:
+ s = ti_read(self.tabixfile, self.iterator, &len)
+ if s == NULL: raise StopIteration
+ if s[0] != '#': break
+
return s
def __dealloc__(self):
if <void*>self.iterator != NULL:
ti_iter_destroy(self.iterator)
-def toDot( v ):
- '''convert value to '.' if None'''
- if v == None: return "."
- else: return str(v)
-
-def quote( v ):
- '''return a quoted attribute.'''
- if type(v) in types.StringTypes:
- return '"%s"' % v
- else:
- return str(v)
-
-cdef class TupleProxy:
- '''Proxy class for access to parsed row as a tuple.
-
- This class represents a table row for fast read-access.
- '''
-
- cdef:
- char * data
- char ** fields
- int nfields
- int index
-
- def __cinit__(self ):
-
- self.data = NULL
- self.fields = NULL
- self.index = 0
-
- cdef take( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Take ownership of the pointer.
- '''
- self.data = buffer
- self.update( buffer, nbytes )
-
- cdef present( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Do not take ownership of the pointer.
- '''
- self.update( buffer, nbytes )
-
- cdef copy( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
+cdef class TabixHeaderIterator:
+ """return header lines.
+ """
+
+ cdef ti_iter_t iterator
+ cdef tabix_t * tabixfile
- Take a copy of buffer.
- '''
- cdef int s
- # +1 for '\0'
- s = sizeof(char) * (nbytes + 1)
- self.data = <char*>malloc( s )
- memcpy( <char*>self.data, buffer, s )
- self.update( self.data, nbytes )
-
- cdef update( self, char * buffer, size_t nbytes ):
- '''update internal data.'''
- cdef char * pos
- cdef char * old_pos
- cdef int field
- cdef int max_fields
- field = 0
-
- if buffer[nbytes] != 0:
- raise ValueError( "incomplete line at %s" % buffer )
+ def __cinit__(self, Tabixfile tabixfile ):
- if self.fields != NULL:
- free(self.fields)
-
- max_fields = nbytes / 4
- self.fields = <char **>calloc( max_fields, sizeof(char *) )
-
- pos = buffer
- self.fields[0] = pos
- field += 1
- old_pos = pos
+ assert tabixfile._isOpen()
- while 1:
-
- pos = <char*>memchr( pos, '\t', nbytes )
- if pos == NULL: break
- pos[0] = '\0'
- pos += 1
- self.fields[field] = pos
- field += 1
- if field >= max_fields:
- raise ValueError("row too large - more than %i fields" % max_fields )
- nbytes -= pos - old_pos
- if nbytes < 0: break
- old_pos = pos
-
- self.nfields = field
-
- def __getitem__( self, key ):
-
- cdef int i
- i = key
- if i < 0: i += self.nfields
- if i >= self.nfields or i < 0:
- raise IndexError( "list index out of range" )
- return self.fields[i]
+ # makes sure that samfile stays alive as long as the
+ # iterator is alive.
+ self.tabixfile = tabixfile.tabixfile
- def __len__(self):
- return self.nfields
+ self.iterator = ti_query(self.tabixfile, NULL, 0, 0)
- def __dealloc__(self):
- if self.data != NULL:
- free(self.data)
+ if <void*>self.iterator == NULL:
+ raise ValueError("can't open header.\n")
def __iter__(self):
- self.index = 0
- return self
+ return self
def __next__(self):
"""python version of next().
- """
- if self.index >= self.nfields:
- raise StopIteration
- self.index += 1
- return self.fields[self.index-1]
-cdef class GTFProxy:
- '''Proxy class for access to GTF fields.
-
- This class represents a GTF entry for fast read-access.
- Write-access has been added as well, though some care must
- be taken. If any of the string fields (contig, source, ...)
- are set, the new value is tied to the lifetime of the
- argument that was supplied.
-
- The only exception is the attributes field when set from
- a dictionary - this field will manage its own memory.
-
- '''
-
- cdef:
- char * contig
- char * source
- char * feature
- uint32_t start
- uint32_t end
- char * score
- char * strand
- char * frame
- char * attributes
- int nbytes
- char * data
- cdef bint isModified
- cdef bint hasOwnAttributes
-
- def __cinit__(self ):
- self.data = NULL
- self.isModified = False
- self.hasOwnAttributes = False
-
- cdef take( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Take ownership of the pointer.
- '''
- self.data = buffer
- self.update( buffer, nbytes )
- self.isModified = False
-
- cdef present( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Do not take ownership of the pointer.
- '''
- self.update( buffer, nbytes )
- self.isModified = False
-
- cdef copy( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Take a copy of buffer.
- '''
- cdef int s
- # +1 for '\0'
- s = sizeof(char) * (nbytes + 1)
- self.data = <char*>malloc( s )
- memcpy( <char*>self.data, buffer, s )
- self.update( self.data, nbytes )
- self.isModified = False
-
- cdef update( self, char * buffer, size_t nbytes ):
- '''update internal data.
-
- nbytes does not include the terminal '\0'.
- '''
- cdef int end
- cdef char * cstart, * cend, * cscore
- self.contig = buffer
- self.nbytes = nbytes
- cdef char * pos
-
- if buffer[nbytes] != 0:
- raise ValueError( "incomplete line at %s" % buffer )
-
- pos = strchr( buffer, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.source = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.feature = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- cstart = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- cend = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.score = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.strand = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.frame = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.attributes = pos
- self.start = atoi( cstart ) - 1
- self.end = atoi( cend )
-
- property contig:
- '''contig of feature.'''
- def __get__( self ): return self.contig
- def __set__( self, value ):
- self.isModified = True
- self.contig = value
-
- property feature:
- '''feature name.'''
- def __get__( self ): return self.feature
- def __set__( self, value ):
- self.isModified = True
- self.feature = value
-
- property source:
- '''feature source.'''
- def __get__( self ): return self.source
- def __set__( self, value ):
- self.isModified = True
- self.source = value
-
- property start:
- '''feature start (in 0-based open/closed coordinates).'''
- def __get__( self ): return self.start
- def __set__( self, value ):
- self.isModified = True
- self.start = value
-
- property end:
- '''feature end (in 0-based open/closed coordinates).'''
- def __get__( self ): return self.end
- def __set__( self, value ):
- self.isModified = True
- self.end = value
-
- property score:
- '''feature score.'''
- def __get__( self ):
- if self.score[0] == '.' and self.score[1] == '\0' :
- return None
- else:
- return atof(self.score)
- def __set__( self, value ):
- self.isModified = True
- self.score = value
-
- property strand:
- '''feature strand.'''
- def __get__( self ): return self.strand
- def __set__( self, value ):
- self.isModified = True
- self.strand = value
-
- property frame:
- '''feature frame.'''
- def __get__( self ): return self.frame
- def __set__( self, value ):
- self.isModified = True
- self.frame = value
-
- property attributes:
- '''feature attributes (as a string).'''
- def __get__( self ): return self.attributes
- def __set__( self, value ):
- self.isModified = True
- self.attributes = value
-
- def asDict( self ):
- """parse attributes - return as dict
+ pyrex uses this non-standard name instead of next()
"""
-
- # remove comments
- attributes = self.attributes
-
- # separate into fields
- fields = [ x.strip() for x in attributes.split(";")[:-1]]
-
- result = {}
-
- for f in fields:
-
- d = [ x.strip() for x in f.split(" ")]
-
- n,v = d[0], d[1]
- if len(d) > 2: v = d[1:]
-
- if v[0] == '"' and v[-1] == '"':
- v = v[1:-1]
- else:
- ## try to convert to a value
- try:
- v = float( v )
- v = int( v )
- except ValueError:
- pass
- except TypeError:
- pass
-
- result[n] = v
-
- return result
- def fromDict( self, d ):
- '''set attributes from a dictionary.'''
- cdef char * p
- cdef int l
-
- # clean up if this field is set twice
- if self.hasOwnAttributes:
- free(self.attributes)
-
- aa = []
- for k,v in d.items():
- if type(v) == types.StringType:
- aa.append( '%s "%s"' % (k,v) )
- else:
- aa.append( '%s %s' % (k,str(v)) )
-
- a = "; ".join( aa ) + ";"
- p = a
- l = len(a)
- self.attributes = <char *>calloc( l + 1, sizeof(char) )
- memcpy( self.attributes, p, l )
-
- self.hasOwnAttributes = True
- self.isModified = True
-
- def __str__(self):
- cdef char * cpy
- cdef int x
-
- if self.isModified:
- return "\t".join(
- (self.contig,
- self.source,
- self.feature,
- str(self.start+1),
- str(self.end),
- toDot(self.score),
- self.strand,
- self.frame,
- self.attributes ) )
- else:
- cpy = <char*>calloc( sizeof(char), self.nbytes+1 )
- memcpy( cpy, self.data, self.nbytes+1)
- for x from 0 <= x < self.nbytes:
- if cpy[x] == '\0': cpy[x] = '\t'
- result = cpy
- free(cpy)
- return result
-
- def invert( self, int lcontig ):
- '''invert coordinates to negative strand coordinates
-
- This method will only act if the feature is on the
- negative strand.'''
-
- if self.strand[0] == '-':
- start = min(self.start, self.end)
- end = max(self.start, self.end)
- self.start, self.end = lcontig - end, lcontig - start
+ cdef char * s
+ cdef int len
- def keys( self ):
- '''return a list of attributes defined in this entry.'''
- r = self.attributes
- return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ]
+ # 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)
+ if s == NULL: raise StopIteration
+ # stop at first non-header line
+ if s[0] != '#': raise StopIteration
- def __getitem__(self, item):
- return self.__getattr__( item )
+ return s
def __dealloc__(self):
- if self.data != NULL:
- free(self.data)
- if self.hasOwnAttributes:
- free(self.attributes)
-
- def __getattr__(self, item ):
- """Generic lookup of attribute from GFF/GTF attributes
- Only called if there *isn't* an attribute with this name
- """
- cdef char * start
- cdef char * query
- cdef char * cpy
- cdef char * end
- cdef int l
- query = item
-
- start = strstr( self.attributes, query)
- if start == NULL:
- raise AttributeError("'GTFProxy' has no attribute '%s'" % item )
-
- start += strlen(query) + 1
- # skip gaps before
- while start[0] == " ": start += 1
- if start[0] == '"':
- start += 1
- end = start
- while end[0] != '\0' and end[0] != '"': end += 1
- l = end - start + 1
- cpy = <char*>calloc( l, sizeof(char ) )
- memcpy( cpy, start, l )
- cpy[l-1] = '\0'
- result = cpy
- free(cpy)
- return result
- else:
- return start
-
- def setAttribute( self, name, value ):
- '''convenience method to set an attribute.'''
- r = self.asDict()
- r[name] = value
- self.fromDict( r )
+ if <void*>self.iterator != NULL:
+ ti_iter_destroy(self.iterator)
+#########################################################
+#########################################################
+#########################################################
cdef class Parser:
pass
cdef class asTuple(Parser):
'''converts a :term:`tabix row` into a python tuple.'''
def __call__(self, char * buffer, int len):
- cdef TupleProxy r
- r = TupleProxy()
+ cdef TabProxies.TupleProxy r
+ r = TabProxies.TupleProxy()
# need to copy - there were some
# persistence issues with "present"
r.copy( buffer, len )
cdef class asGTF(Parser):
'''converts a :term:`tabix row` into a GTF record.'''
def __call__(self, char * buffer, int len):
- cdef GTFProxy r
- r = GTFProxy()
+ cdef TabProxies.GTFProxy r
+ r = TabProxies.GTFProxy()
r.copy( buffer, len )
return r
+cdef class asBed( Parser ):
+ '''converts a :term:`tabix row` into a GTF record.'''
+ def __call__(self, char * buffer, int len):
+ cdef TabProxies.BedProxy r
+ r = TabProxies.BedProxy()
+ r.copy( buffer, len )
+ return r
+
+cdef class asVCF( Parser ):
+ '''converts a :term:`tabix row` into a VCF record.'''
+ def __call__(self, char * buffer, int len ):
+ cdef TabProxies.VCFProxy r
+ r = TabProxies.VCFProxy()
+ r.copy( buffer, len )
+ return r
+
+#########################################################
+#########################################################
+#########################################################
cdef class TabixIteratorParsed:
"""iterates over mapped reads in a region.
+
+ Returns parsed data.
"""
-
+
cdef ti_iter_t iterator
cdef tabix_t * tabixfile
cdef Parser parser
cdef char * s
cdef int len
- s = ti_read(self.tabixfile, self.iterator, &len)
- if s == NULL: raise StopIteration
+ while 1:
+ s = ti_read(self.tabixfile, self.iterator, &len)
+ if s == NULL: raise StopIteration
+ # todo: read metachar from configuration
+ if s[0] != '#': break
+
return self.parser(s, len)
def __dealloc__(self):
"Tabixfile",
"asTuple",
"asGTF",
+ "asVCF",
+ "asBed",
]
--- /dev/null
+/* Generated by Cython 0.13 on Thu May 5 15:40:49 2011 */
+
+#define PY_SSIZE_T_CLEAN
+#include "Python.h"
+#ifndef Py_PYTHON_H
+ #error Python headers needed to compile C extensions, please install development version of Python.
+#else
+
+#include <stddef.h> /* For offsetof */
+#ifndef offsetof
+#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
+#endif
+
+#if !defined(WIN32) && !defined(MS_WINDOWS)
+ #ifndef __stdcall
+ #define __stdcall
+ #endif
+ #ifndef __cdecl
+ #define __cdecl
+ #endif
+ #ifndef __fastcall
+ #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
+
+#if PY_VERSION_HEX < 0x02040000
+ #define METH_COEXIST 0
+ #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
+ #define PyDict_Contains(d,o) PySequence_Contains(d,o)
+#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 PyInt_FromSsize_t(z) PyInt_FromLong(z)
+ #define PyInt_AsSsize_t(o) PyInt_AsLong(o)
+ #define PyNumber_Index(o) PyNumber_Int(o)
+ #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
+ #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
+ #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
+ #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
+ #define PyVarObject_HEAD_INIT(type, size) \
+ PyObject_HEAD_INIT(type) size,
+ #define PyType_Modified(t)
+
+ typedef struct {
+ void *buf;
+ PyObject *obj;
+ Py_ssize_t len;
+ Py_ssize_t itemsize;
+ int readonly;
+ int ndim;
+ char *format;
+ Py_ssize_t *shape;
+ Py_ssize_t *strides;
+ Py_ssize_t *suboffsets;
+ void *internal;
+ } Py_buffer;
+
+ #define PyBUF_SIMPLE 0
+ #define PyBUF_WRITABLE 0x0001
+ #define PyBUF_FORMAT 0x0004
+ #define PyBUF_ND 0x0008
+ #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
+ #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
+ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
+ #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
+ #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
+
+#endif
+
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+#else
+ #define __Pyx_BUILTIN_MODULE_NAME "builtins"
+#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_MAJOR_VERSION >= 3
+ #define PyBaseString_Type PyUnicode_Type
+ #define PyStringObject PyUnicodeObject
+ #define PyString_Type PyUnicode_Type
+ #define PyString_Check PyUnicode_Check
+ #define PyString_CheckExact PyUnicode_CheckExact
+#endif
+
+#if PY_VERSION_HEX < 0x02060000
+ #define PyBytesObject PyStringObject
+ #define PyBytes_Type PyString_Type
+ #define PyBytes_Check PyString_Check
+ #define PyBytes_CheckExact PyString_CheckExact
+ #define PyBytes_FromString PyString_FromString
+ #define PyBytes_FromStringAndSize PyString_FromStringAndSize
+ #define PyBytes_FromFormat PyString_FromFormat
+ #define PyBytes_DecodeEscape PyString_DecodeEscape
+ #define PyBytes_AsString PyString_AsString
+ #define PyBytes_AsStringAndSize PyString_AsStringAndSize
+ #define PyBytes_Size PyString_Size
+ #define PyBytes_AS_STRING PyString_AS_STRING
+ #define PyBytes_GET_SIZE PyString_GET_SIZE
+ #define PyBytes_Repr PyString_Repr
+ #define PyBytes_Concat PyString_Concat
+ #define PyBytes_ConcatAndDel PyString_ConcatAndDel
+ #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
+ #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
+#endif
+
+#ifndef PySet_CheckExact
+# define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyInt_Type PyLong_Type
+ #define PyInt_Check(op) PyLong_Check(op)
+ #define PyInt_CheckExact(op) PyLong_CheckExact(op)
+ #define PyInt_FromString PyLong_FromString
+ #define PyInt_FromUnicode PyLong_FromUnicode
+ #define PyInt_FromLong PyLong_FromLong
+ #define PyInt_FromSize_t PyLong_FromSize_t
+ #define PyInt_FromSsize_t PyLong_FromSsize_t
+ #define PyInt_AsLong PyLong_AsLong
+ #define PyInt_AS_LONG PyLong_AS_LONG
+ #define PyInt_AsSsize_t PyLong_AsSsize_t
+ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
+ #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
+#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define PyBoolObject PyLongObject
+#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)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#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))
+ #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
+#else
+ #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
+ #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))
+#else
+ #define __Pyx_NAMESTR(n) (n)
+ #define __Pyx_DOCSTR(n) (n)
+#endif
+
+#ifdef __cplusplus
+#define __PYX_EXTERN_C extern "C"
+#else
+#define __PYX_EXTERN_C extern
+#endif
+
+#if defined(WIN32) || defined(MS_WINDOWS)
+#define _USE_MATH_DEFINES
+#endif
+#include <math.h>
+#define __PYX_HAVE_API__cvcf
+#include "stdlib.h"
+#include "string.h"
+#include "stdint.h"
+#include "stdio.h"
+#include "ctype.h"
+#include "sys/types.h"
+#include "sys/stat.h"
+#include "fcntl.h"
+#include "unistd.h"
+#include "bgzf.h"
+#include "tabix.h"
+
+/* inline attribute */
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
+
+/* unused attribute */
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || defined(__INTEL_COMPILER)
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+
+typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
+
+
+/* Type Conversion Predeclarations */
+
+#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
+#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
+
+#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
+
+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*);
+
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+
+
+#ifdef __GNUC__
+/* Test for GCC > 2.95 */
+#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
+#define likely(x) __builtin_expect(!!(x), 1)
+#define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* __GNUC__ > 2 ... */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ > 2 ... */
+#else /* __GNUC__ */
+#define likely(x) (x)
+#define unlikely(x) (x)
+#endif /* __GNUC__ */
+
+static PyObject *__pyx_m;
+static PyObject *__pyx_b;
+static PyObject *__pyx_empty_tuple;
+static PyObject *__pyx_empty_bytes;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+
+
+static const char *__pyx_f[] = {
+ "cvcf.pyx",
+ "ctabix.pxd",
+ "TabProxies.pxd",
+};
+
+/* Type declarations */
+
+/* "pysam/TabProxies.pxd":42
+ * ctypedef int uint64_t
+ *
+ * cdef class TupleProxy: # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_obj_10TabProxies_TupleProxy {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
+ char *data;
+ char **fields;
+ int nfields;
+ int index;
+ int nbytes;
+ int offset;
+ int is_modified;
+};
+
+/* "pysam/TabProxies.pxd":77
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_obj_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+};
+
+/* "pysam/TabProxies.pxd":80
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_obj_10TabProxies_BedProxy {
+ struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+ * ###########################################################################################################
+ *
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
+ */
+
+struct __pyx_obj_4cvcf_VCFRecord {
+ struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+ PyObject *vcf;
+ char *contig;
+ uint32_t pos;
+};
+
+/* "pysam/TabProxies.pxd":91
+ * 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;
+};
+
+/* "pysam/ctabix.pxd":178
+ * cdef tabix_t * tabixfile
+ *
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
+ */
+
+struct __pyx_obj_6ctabix_Parser {
+ PyObject_HEAD
+};
+
+/* "pysam/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 *contig;
+ char *source;
+ char *feature;
+ uint32_t start;
+ uint32_t end;
+ char *score;
+ char *strand;
+ char *frame;
+ char *attributes;
+ int hasOwnAttributes;
+};
+
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":221
+ *
+ *
+ * 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;
+ PyObject *vcffile;
+};
+
+/* "pysam/ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+ *
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ * cdef char * filename
+ *
+ */
+
+struct __pyx_obj_6ctabix_Tabixfile {
+ PyObject_HEAD
+ char *filename;
+ tabix_t *tabixfile;
+};
+
+
+/* "pysam/TabProxies.pxd":42
+ * ctypedef int uint64_t
+ *
+ * cdef class TupleProxy: # <<<<<<<<<<<<<<
+ *
+ * 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);
+};
+static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
+
+
+/* "pysam/TabProxies.pxd":77
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+
+struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+
+
+/* "pysam/TabProxies.pxd":91
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+
+
+/* "pysam/TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
+
+
+/* "/ifs/devel/pysam/pysam/pysam/cvcf.pyx":94
+ * ###########################################################################################################
+ *
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
+ */
+
+struct __pyx_vtabstruct_4cvcf_VCFRecord {
+ struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
+
+
+/* "pysam/TabProxies.pxd":80
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+
+struct __pyx_vtabstruct_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
+
+#ifndef CYTHON_REFNANNY
+ #define CYTHON_REFNANNY 0
+#endif
+
+#if CYTHON_REFNANNY
+ typedef struct {
+ void (*INCREF)(void*, PyObject*, int);
+ void (*DECREF)(void*, PyObject*, int);
+ void (*GOTREF)(void*, PyObject*, int);
+ void (*GIVEREF)(void*, PyObject*, int);
+ void* (*SetupContext)(const char*, int, const char*);
+ void (*FinishContext)(void**);
+ } __Pyx_RefNannyAPIStruct;
+ static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
+ static __Pyx_RefNannyAPIStruct * __Pyx_RefNannyImportAPI(const char *modname) {
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+ void *r = NULL;
+ m = PyImport_ImportModule((char *)modname);
+ if (!m) goto end;
+ p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
+ if (!p) goto end;
+ r = PyLong_AsVoidPtr(p);
+ end:
+ Py_XDECREF(p);
+ Py_XDECREF(m);
+ return (__Pyx_RefNannyAPIStruct *)r;
+ }
+ #define __Pyx_RefNannySetupContext(name) void *__pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
+ #define __Pyx_RefNannyFinishContext() __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
+ #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
+ #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r);} } while(0)
+#else
+ #define __Pyx_RefNannySetupContext(name)
+ #define __Pyx_RefNannyFinishContext()
+ #define __Pyx_INCREF(r) Py_INCREF(r)
+ #define __Pyx_DECREF(r) Py_DECREF(r)
+ #define __Pyx_GOTREF(r)
+ #define __Pyx_GIVEREF(r)
+ #define __Pyx_XDECREF(r) Py_XDECREF(r)
+#endif /* CYTHON_REFNANNY */
+#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);} } while(0)
+#define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r);} } while(0)
+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name, PyObject* kw_name); /*proto*/
+
+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
+
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
+
+
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+
+
+#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __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;
+ }
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
+#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;
+ }
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
+
+#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) {
+ PyObject *r;
+ if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
+ r = PySequence_GetItem(o, i);
+ }
+ else {
+ r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ }
+ return r;
+}
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
+static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
+
+#define __Pyx_PyObject_AsDouble(obj) \
+ ((likely(PyFloat_CheckExact(obj))) ? \
+ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
+
+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())
+ PyErr_SetObject(PyExc_KeyError, key);
+ return NULL;
+ }
+ Py_INCREF(value);
+ return value;
+}
+#else
+ #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
+#endif
+
+static CYTHON_INLINE long __Pyx_NegateNonNeg(long 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 void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+static PyObject *__Pyx_UnpackItem(PyObject *, Py_ssize_t index); /*proto*/
+static int __Pyx_EndUnpack(PyObject *, Py_ssize_t expected); /*proto*/
+
+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;
+ Py_INCREF(Py_None);
+ return Py_None; /* this is just to have an accurate signature */
+ }
+ else {
+ PyObject *r, *m;
+ m = __Pyx_GetAttrString(L, "append");
+ if (!m) return NULL;
+ r = PyObject_CallFunctionObjArgs(m, x, NULL);
+ Py_DECREF(m);
+ return r;
+ }
+}
+
+#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))
+
+static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
+ int r;
+ if (!j) return -1;
+ r = PyObject_SetItem(o, j, v);
+ Py_DECREF(j);
+ return r;
+}
+
+static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
+ if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ Py_INCREF(v);
+ Py_DECREF(PyList_GET_ITEM(o, i));
+ PyList_SET_ITEM(o, i, v);
+ return 1;
+ }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && (likely(i >= 0)))
+ return PySequence_SetItem(o, i, v);
+ else {
+ PyObject *j = PyInt_FromSsize_t(i);
+ return __Pyx_SetItemInt_Generic(o, j, v);
+ }
+}
+
+#if PY_VERSION_HEX < 0x02050000
+#ifndef PyAnySet_CheckExact
+
+#define PyAnySet_CheckExact(ob) \
+ ((ob)->ob_type == &PySet_Type || \
+ (ob)->ob_type == &PyFrozenSet_Type)
+
+#define PySet_New(iterable) \
+ PyObject_CallFunctionObjArgs((PyObject *)&PySet_Type, (iterable), NULL)
+
+#define Pyx_PyFrozenSet_New(iterable) \
+ PyObject_CallFunctionObjArgs((PyObject *)&PyFrozenSet_Type, (iterable), NULL)
+
+#define PySet_Size(anyset) \
+ PyObject_Size((anyset))
+
+#define PySet_Contains(anyset, key) \
+ PySequence_Contains((anyset), (key))
+
+#define PySet_Pop(set) \
+ PyObject_CallMethod(set, (char *)"pop", NULL)
+
+static CYTHON_INLINE int PySet_Clear(PyObject *set) {
+ PyObject *ret = PyObject_CallMethod(set, (char *)"clear", NULL);
+ if (!ret) return -1;
+ Py_DECREF(ret); return 0;
+}
+
+static CYTHON_INLINE int PySet_Discard(PyObject *set, PyObject *key) {
+ PyObject *ret = PyObject_CallMethod(set, (char *)"discard", (char *)"O", key);
+ if (!ret) return -1;
+ Py_DECREF(ret); return 0;
+}
+
+static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) {
+ PyObject *ret = PyObject_CallMethod(set, (char *)"add", (char *)"O", key);
+ if (!ret) return -1;
+ Py_DECREF(ret); return 0;
+}
+
+#endif /* PyAnySet_CheckExact (<= Py2.4) */
+
+#if PY_VERSION_HEX < 0x02040000
+#ifndef Py_SETOBJECT_H
+#define Py_SETOBJECT_H
+
+static PyTypeObject *__Pyx_PySet_Type = NULL;
+static PyTypeObject *__Pyx_PyFrozenSet_Type = NULL;
+
+#define PySet_Type (*__Pyx_PySet_Type)
+#define PyFrozenSet_Type (*__Pyx_PyFrozenSet_Type)
+
+#define PyAnySet_Check(ob) \
+ (PyAnySet_CheckExact(ob) || \
+ PyType_IsSubtype((ob)->ob_type, &PySet_Type) || \
+ PyType_IsSubtype((ob)->ob_type, &PyFrozenSet_Type))
+
+#define PyFrozenSet_CheckExact(ob) ((ob)->ob_type == &PyFrozenSet_Type)
+
+static int __Pyx_Py23SetsImport(void) {
+ PyObject *sets=0, *Set=0, *ImmutableSet=0;
+
+ sets = PyImport_ImportModule((char *)"sets");
+ if (!sets) goto bad;
+ Set = PyObject_GetAttrString(sets, (char *)"Set");
+ if (!Set) goto bad;
+ ImmutableSet = PyObject_GetAttrString(sets, (char *)"ImmutableSet");
+ if (!ImmutableSet) goto bad;
+ Py_DECREF(sets);
+
+ __Pyx_PySet_Type = (PyTypeObject*) Set;
+ __Pyx_PyFrozenSet_Type = (PyTypeObject*) ImmutableSet;
+
+ return 0;
+
+ bad:
+ Py_XDECREF(sets);
+ Py_XDECREF(Set);
+ Py_XDECREF(ImmutableSet);
+ return -1;
+}
+
+#else
+static int __Pyx_Py23SetsImport(void) { return 0; }
+#endif /* !Py_SETOBJECT_H */
+#endif /* < Py2.4 */
+#endif /* < Py2.5 */
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list); /*proto*/
+
+static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, const char *modname); /*proto*/
+
+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*/
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+
+static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *);
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *);
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *);
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *);
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *);
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *);
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *);
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *);
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *);
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *);
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *);
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size, int strict); /*proto*/
+
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
+static int __Pyx_GetVtable(PyObject *dict, void *vtabptr); /*proto*/
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
+
+static void __Pyx_AddTraceback(const char *funcname); /*proto*/
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+/* Module declarations from ctabix */
+
+static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0;
+static PyTypeObject *__pyx_ptype_6ctabix_Parser = 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;
+#define __Pyx_MODULE_NAME "cvcf"
+int __pyx_module_is_main_cvcf = 0;
+
+/* Implementation of cvcf */
+static PyObject *__pyx_builtin_object;
+static PyObject *__pyx_builtin_ValueError;
+static PyObject *__pyx_builtin_range;
+static PyObject *__pyx_builtin_enumerate;
+static PyObject *__pyx_builtin_map;
+static PyObject *__pyx_builtin_min;
+static PyObject *__pyx_builtin_len;
+static PyObject *__pyx_builtin_zip;
+static PyObject *__pyx_builtin_StopIteration;
+static PyObject *__pyx_builtin_KeyError;
+static PyObject *__pyx_builtin_NotImplementedError;
+static char __pyx_k_1[] = "";
+static char __pyx_k_2[] = ",";
+static char __pyx_k_3[] = ":";
+static char __pyx_k_4[] = "-";
+static char __pyx_k_5[] = "Don't understand region string '%s'";
+static char __pyx_k_6[] = ".";
+static char __pyx_k_7[] = ";";
+static char __pyx_k_8[] = "=";
+static char __pyx_k_9[] = "BAD_NUMBER_OF_VALUES";
+static char __pyx_k_10[] = "(found %s values in element %s; expected %s)";
+static char __pyx_k_11[] = "BAD_NUMBER_OF_PARAMETERS";
+static char __pyx_k_12[] = "id=%s, expected %s parameters, got %s";
+static char __pyx_k_14[] = "Line %s: '%s'\n%s %s: %s\n";
+static char __pyx_k_16[] = "<";
+static char __pyx_k_17[] = "V40_MISSING_ANGLE_BRACKETS";
+static char __pyx_k_18[] = ">";
+static char __pyx_k_19[] = "\"";
+static char __pyx_k_20[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
+static char __pyx_k_21[] = "BADLY_FORMATTED_FORMAT_STRING";
+static char __pyx_k_22[] = "ID=";
+static char __pyx_k_23[] = "Number=";
+static char __pyx_k_24[] = "Type=";
+static char __pyx_k_25[] = "Description=";
+static char __pyx_k_26[] = "FORMAT_MISSING_QUOTES";
+static char __pyx_k_27[] = "<none>";
+static char __pyx_k_28[] = "#alleles";
+static char __pyx_k_29[] = "#nonref_alleles";
+static char __pyx_k_30[] = "#genotypes";
+static char __pyx_k_31[] = "#phased_genotypes";
+static char __pyx_k_33[] = "Unknown number type encountered: %s";
+static char __pyx_k_34[] = "%s=%s";
+static char __pyx_k_35[] = "(Undefined tag)";
+static char __pyx_k_38[] = "(output)";
+static char __pyx_k_39[] = "Genotype Quality";
+static char __pyx_k_40[] = "Read depth at this position for this sample";
+static char __pyx_k_41[] = "Haplotype Quality";
+static char __pyx_k_42[] = "Sample Genotype Filter";
+static char __pyx_k_43[] = "##";
+static char __pyx_k_44[] = "VCFv3.3";
+static char __pyx_k_45[] = "VCFv4.0";
+static char __pyx_k_46[] = "VCFv4.1";
+static char __pyx_k_47[] = "UNKNOWN_FORMAT_STRING";
+static char __pyx_k_48[] = "##fileformat=VCFv%s.%s\n";
+static char __pyx_k_49[] = "##%s=%s\n";
+static char __pyx_k_50[] = "#";
+static char __pyx_k_51[] = "\t";
+static char __pyx_k_52[] = "HEADING_NOT_SEPARATED_BY_TABS";
+static char __pyx_k_53[] = "(%sth entry not found)";
+static char __pyx_k_54[] = "(found %s, expected %s)";
+static char __pyx_k_55[] = "BADLY_FORMATTED_HEADING";
+static char __pyx_k_56[] = "\n";
+static char __pyx_k_57[] = "|";
+static char __pyx_k_58[] = "ERROR_FLAG_HAS_VALUE";
+static char __pyx_k_59[] = "ERROR_FORMAT_NOT_NUMERICAL";
+static char __pyx_k_60[] = "ERROR_FORMAT_NOT_CHAR";
+static char __pyx_k_62[] = "BAD_NUMBER_OF_COLUMNS";
+static char __pyx_k_63[] = "expected %s for %s samples (%s), got %s";
+static char __pyx_k_64[] = "(reference is %s, VCF says %s)";
+static char __pyx_k_65[] = "V33_UNMATCHED_DELETION";
+static char __pyx_k_66[] = "(deletion is %s, reference is %s)";
+static char __pyx_k_67[] = "MISSING_INDEL_ALLELE_REF_BASE";
+static char __pyx_k_68[] = "Required key %s not found in data";
+static char __pyx_k_69[] = "enter_default_format";
+static char __pyx_k_70[] = "Can only handle v3.3 and v4.0 VCF files";
+static char __pyx_k_71[] = "Invalid error string: %s";
+static char __pyx_k_72[] = "needs to be checked";
+static char __pyx_k_73[] = "[|/\\\\]";
+static char __pyx_k_74[] = "^[ACGTN]+$";
+static char __pyx_k_75[] = "id numbertype number type description missingvalue";
+static char __pyx_k_76[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
+static char __pyx_k_77[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
+static char __pyx_k_78[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
+static char __pyx_k_79[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
+static char __pyx_k_80[] = "POS_NOT_NUMERICAL:Position column is not numerical";
+static char __pyx_k_81[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
+static char __pyx_k_82[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
+static char __pyx_k_83[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
+static char __pyx_k_84[] = "POS_NOT_POSITIVE:Position field must be >0";
+static char __pyx_k_85[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
+static char __pyx_k_86[] = "ERROR_INFO_STRING:Error while parsing info field";
+static char __pyx_k_87[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
+static char __pyx_k_88[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
+static char __pyx_k_89[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
+static char __pyx_k_90[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
+static char __pyx_k_91[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
+static char __pyx_k_92[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
+static char __pyx_k_93[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
+static char __pyx_k_94[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
+static char __pyx_k_95[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
+static char __pyx_k_96[] = "MISSING_REF:Reference allele missing";
+static char __pyx_k_97[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
+static char __pyx_k_98[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
+static char __pyx_k_99[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k__0[] = "0";
+static char __pyx_k__D[] = "D";
+static char __pyx_k__I[] = "I";
+static char __pyx_k__N[] = "N";
+static char __pyx_k_100[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
+static char __pyx_k_101[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
+static char __pyx_k_102[] = "WRONG_REF:Wrong reference %s";
+static char __pyx_k_103[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
+static char __pyx_k_104[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
+static char __pyx_k_105[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
+static char __pyx_k_106[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
+static char __pyx_k_107[] = "VCF.getsamples (line 880)";
+static char __pyx_k_108[] = "VCF.setsamples (line 884)";
+static char __pyx_k_109[] = "VCF.getheader (line 888)";
+static char __pyx_k_110[] = "VCF.setheader (line 892)";
+static char __pyx_k_111[] = "VCF.getinfo (line 896)";
+static char __pyx_k_112[] = "VCF.setinfo (line 900)";
+static char __pyx_k_113[] = "VCF.getformat (line 904)";
+static char __pyx_k_114[] = "VCF.setformat (line 908)";
+static char __pyx_k_115[] = "VCF.getfilter (line 912)";
+static char __pyx_k_116[] = "VCF.setfilter (line 916)";
+static char __pyx_k_117[] = "VCF.setreference (line 927)";
+static char __pyx_k_118[] = "VCF.parse (line 939)";
+static char __pyx_k_119[] = "VCF.write (line 946)";
+static char __pyx_k_120[] = "VCF.writeheader (line 952)";
+static char __pyx_k_121[] = "VCF.compare_calls (line 957)";
+static char __pyx_k_122[] = "VCF.connect (line 979)";
+static char __pyx_k_123[] = "VCF.fetch (line 984)";
+static char __pyx_k_124[] = "VCF.validate (line 993)";
+static char __pyx_k__DP[] = "DP";
+static char __pyx_k__FT[] = "FT";
+static char __pyx_k__GQ[] = "GQ";
+static char __pyx_k__GT[] = "GT";
+static char __pyx_k__HQ[] = "HQ";
+static char __pyx_k__ID[] = "ID";
+static char __pyx_k__fa[] = "fa";
+static char __pyx_k__id[] = "id";
+static char __pyx_k__re[] = "re";
+static char __pyx_k__ALT[] = "ALT";
+static char __pyx_k__POS[] = "POS";
+static char __pyx_k__REF[] = "REF";
+static char __pyx_k__VCF[] = "VCF";
+static char __pyx_k__add[] = "add";
+static char __pyx_k__alt[] = "alt";
+static char __pyx_k__end[] = "end";
+static char __pyx_k__fmt[] = "fmt";
+static char __pyx_k__get[] = "get";
+static char __pyx_k__key[] = "key";
+static char __pyx_k__len[] = "len";
+static char __pyx_k__map[] = "map";
+static char __pyx_k__min[] = "min";
+static char __pyx_k__opt[] = "opt";
+static char __pyx_k__pos[] = "pos";
+static char __pyx_k__ref[] = "ref";
+static char __pyx_k__sys[] = "sys";
+static char __pyx_k__vcf[] = "vcf";
+static char __pyx_k__zip[] = "zip";
+static char __pyx_k__Flag[] = "Flag";
+static char __pyx_k__INFO[] = "INFO";
+static char __pyx_k__PASS[] = "PASS";
+static char __pyx_k__QUAL[] = "QUAL";
+static char __pyx_k__Type[] = "Type";
+static char __pyx_k__alt1[] = "alt1";
+static char __pyx_k__alt2[] = "alt2";
+static char __pyx_k__copy[] = "copy";
+static char __pyx_k__data[] = "data";
+static char __pyx_k__find[] = "find";
+static char __pyx_k__info[] = "info";
+static char __pyx_k__join[] = "join";
+static char __pyx_k__keys[] = "keys";
+static char __pyx_k__line[] = "line";
+static char __pyx_k__pos1[] = "pos1";
+static char __pyx_k__pos2[] = "pos2";
+static char __pyx_k__qual[] = "qual";
+static char __pyx_k__ref1[] = "ref1";
+static char __pyx_k__ref2[] = "ref2";
+static char __pyx_k__self[] = "self";
+static char __pyx_k__type[] = "type";
+static char __pyx_k__ACGTN[] = "ACGTN";
+static char __pyx_k__CHROM[] = "CHROM";
+static char __pyx_k__Error[] = "Error";
+static char __pyx_k__Float[] = "Float";
+static char __pyx_k___copy[] = "_copy";
+static char __pyx_k___info[] = "_info";
+static char __pyx_k___line[] = "_line";
+static char __pyx_k__chrom[] = "chrom";
+static char __pyx_k__descr[] = "descr";
+static char __pyx_k__error[] = "error";
+static char __pyx_k__fetch[] = "fetch";
+static char __pyx_k__lines[] = "lines";
+static char __pyx_k__match[] = "match";
+static char __pyx_k__parse[] = "parse";
+static char __pyx_k__pysam[] = "pysam";
+static char __pyx_k__range[] = "range";
+static char __pyx_k__split[] = "split";
+static char __pyx_k__start[] = "start";
+static char __pyx_k__strip[] = "strip";
+static char __pyx_k__upper[] = "upper";
+static char __pyx_k__value[] = "value";
+static char __pyx_k__write[] = "write";
+static char __pyx_k__FILTER[] = "FILTER";
+static char __pyx_k__FORMAT[] = "FORMAT";
+static char __pyx_k__GTdata[] = "GTdata";
+static char __pyx_k__Number[] = "Number";
+static char __pyx_k__String[] = "String";
+static char __pyx_k___lines[] = "_lines";
+static char __pyx_k___parse[] = "_parse";
+static char __pyx_k__bisect[] = "bisect";
+static char __pyx_k__buffer[] = "buffer";
+static char __pyx_k__contig[] = "contig";
+static char __pyx_k__fields[] = "fields";
+static char __pyx_k__filter[] = "filter";
+static char __pyx_k__format[] = "format";
+static char __pyx_k__header[] = "header";
+static char __pyx_k__number[] = "number";
+static char __pyx_k__object[] = "object";
+static char __pyx_k__offset[] = "offset";
+static char __pyx_k__parser[] = "parser";
+static char __pyx_k__record[] = "record";
+static char __pyx_k__region[] = "region";
+static char __pyx_k__stderr[] = "stderr";
+static char __pyx_k__stream[] = "stream";
+static char __pyx_k__Integer[] = "Integer";
+static char __pyx_k__Warning[] = "Warning";
+static char __pyx_k____all__[] = "__all__";
+static char __pyx_k___errors[] = "_errors";
+static char __pyx_k___filter[] = "_filter";
+static char __pyx_k___format[] = "_format";
+static char __pyx_k___header[] = "_header";
+static char __pyx_k___lineno[] = "_lineno";
+static char __pyx_k__compile[] = "compile";
+static char __pyx_k__connect[] = "connect";
+static char __pyx_k__getinfo[] = "getinfo";
+static char __pyx_k__missing[] = "missing";
+static char __pyx_k__nfields[] = "nfields";
+static char __pyx_k__regions[] = "regions";
+static char __pyx_k__replace[] = "replace";
+static char __pyx_k__samples[] = "samples";
+static char __pyx_k__setinfo[] = "setinfo";
+static char __pyx_k__vcffile[] = "vcffile";
+static char __pyx_k__version[] = "version";
+static char __pyx_k__GTstring[] = "GTstring";
+static char __pyx_k__Genotype[] = "Genotype";
+static char __pyx_k__KeyError[] = "KeyError";
+static char __pyx_k____dict__[] = "__dict__";
+static char __pyx_k____init__[] = "__init__";
+static char __pyx_k____main__[] = "__main__";
+static char __pyx_k____test__[] = "__test__";
+static char __pyx_k___regions[] = "_regions";
+static char __pyx_k___samples[] = "_samples";
+static char __pyx_k___version[] = "_version";
+static char __pyx_k__deepcopy[] = "deepcopy";
+static char __pyx_k__endswith[] = "endswith";
+static char __pyx_k__filename[] = "filename";
+static char __pyx_k__gtsRegEx[] = "gtsRegEx";
+static char __pyx_k__inregion[] = "inregion";
+static char __pyx_k__operator[] = "operator";
+static char __pyx_k__validate[] = "validate";
+static char __pyx_k__Character[] = "Character";
+static char __pyx_k__NT_NUMBER[] = "NT_NUMBER";
+static char __pyx_k__Tabixfile[] = "Tabixfile";
+static char __pyx_k__VCFRecord[] = "VCFRecord";
+static char __pyx_k__WRONG_REF[] = "WRONG_REF";
+static char __pyx_k___required[] = "_required";
+static char __pyx_k__convertGT[] = "convertGT";
+static char __pyx_k__enumerate[] = "enumerate";
+static char __pyx_k__getfilter[] = "getfilter";
+static char __pyx_k__getformat[] = "getformat";
+static char __pyx_k__getheader[] = "getheader";
+static char __pyx_k__leftalign[] = "leftalign";
+static char __pyx_k__lineparse[] = "lineparse";
+static char __pyx_k__reference[] = "reference";
+static char __pyx_k__separator[] = "separator";
+static char __pyx_k__setfilter[] = "setfilter";
+static char __pyx_k__setformat[] = "setformat";
+static char __pyx_k__setheader[] = "setheader";
+static char __pyx_k__tabixfile[] = "tabixfile";
+static char __pyx_k__warnerror[] = "warnerror";
+static char __pyx_k__NT_ALLELES[] = "NT_ALLELES";
+static char __pyx_k__NT_UNKNOWN[] = "NT_UNKNOWN";
+static char __pyx_k__ValueError[] = "ValueError";
+static char __pyx_k___leftalign[] = "_leftalign";
+static char __pyx_k___reference[] = "_reference";
+static char __pyx_k__fileformat[] = "fileformat";
+static char __pyx_k__formatdict[] = "formatdict";
+static char __pyx_k__getsamples[] = "getsamples";
+static char __pyx_k__itemgetter[] = "itemgetter";
+static char __pyx_k__itervalues[] = "itervalues";
+static char __pyx_k__namedtuple[] = "namedtuple";
+static char __pyx_k__numbertype[] = "numbertype";
+static char __pyx_k__parse_data[] = "parse_data";
+static char __pyx_k__setregions[] = "setregions";
+static char __pyx_k__setsamples[] = "setsamples";
+static char __pyx_k__setversion[] = "setversion";
+static char __pyx_k__startswith[] = "startswith";
+static char __pyx_k__write_data[] = "write_data";
+static char __pyx_k__Description[] = "Description";
+static char __pyx_k__MISSING_REF[] = "MISSING_REF";
+static char __pyx_k__V33_BAD_REF[] = "V33_BAD_REF";
+static char __pyx_k__alleleRegEx[] = "alleleRegEx";
+static char __pyx_k__collections[] = "collections";
+static char __pyx_k__defaultdict[] = "defaultdict";
+static char __pyx_k__description[] = "description";
+static char __pyx_k__errorstring[] = "errorstring";
+static char __pyx_k__ignoreerror[] = "ignoreerror";
+static char __pyx_k__writeheader[] = "writeheader";
+static char __pyx_k__BAD_GENOTYPE[] = "BAD_GENOTYPE";
+static char __pyx_k__NT_GENOTYPES[] = "NT_GENOTYPES";
+static char __pyx_k___warn_errors[] = "_warn_errors";
+static char __pyx_k__get_expected[] = "get_expected";
+static char __pyx_k__get_sequence[] = "get_sequence";
+static char __pyx_k__missingvalue[] = "missingvalue";
+static char __pyx_k__parse_format[] = "parse_format";
+static char __pyx_k__parse_header[] = "parse_header";
+static char __pyx_k__setreference[] = "setreference";
+static char __pyx_k__write_header[] = "write_header";
+static char __pyx_k__NT_NR_ALLELES[] = "NT_NR_ALLELES";
+static char __pyx_k__StopIteration[] = "StopIteration";
+static char __pyx_k___parse_header[] = "_parse_header";
+static char __pyx_k__compare_calls[] = "compare_calls";
+static char __pyx_k__convertGTback[] = "convertGTback";
+static char __pyx_k__datagenerator[] = "datagenerator";
+static char __pyx_k__format_format[] = "format_format";
+static char __pyx_k__parse_heading[] = "parse_heading";
+static char __pyx_k__write_heading[] = "write_heading";
+static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE";
+static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE";
+static char __pyx_k___sample2column[] = "_sample2column";
+static char __pyx_k___add_definition[] = "_add_definition";
+static char __pyx_k___ignored_errors[] = "_ignored_errors";
+static char __pyx_k__POS_NOT_POSITIVE[] = "POS_NOT_POSITIVE";
+static char __pyx_k__parse_formatdata[] = "parse_formatdata";
+static char __pyx_k__ERROR_INFO_STRING[] = "ERROR_INFO_STRING";
+static char __pyx_k__ERROR_UNKNOWN_KEY[] = "ERROR_UNKNOWN_KEY";
+static char __pyx_k__POS_NOT_NUMERICAL[] = "POS_NOT_NUMERICAL";
+static char __pyx_k__format_formatdata[] = "format_formatdata";
+static char __pyx_k__FILTER_NOT_DEFINED[] = "FILTER_NOT_DEFINED";
+static char __pyx_k__FORMAT_NOT_DEFINED[] = "FORMAT_NOT_DEFINED";
+static char __pyx_k__QUAL_NOT_NUMERICAL[] = "QUAL_NOT_NUMERICAL";
+static char __pyx_k__ZERO_LENGTH_ALLELE[] = "ZERO_LENGTH_ALLELE";
+static char __pyx_k__ERROR_TRAILING_DATA[] = "ERROR_TRAILING_DATA";
+static char __pyx_k__NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES";
+static char __pyx_k__NotImplementedError[] = "NotImplementedError";
+static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF";
+static PyObject *__pyx_kp_s_1;
+static PyObject *__pyx_kp_s_10;
+static PyObject *__pyx_kp_s_100;
+static PyObject *__pyx_kp_s_101;
+static PyObject *__pyx_kp_s_102;
+static PyObject *__pyx_kp_s_103;
+static PyObject *__pyx_kp_s_104;
+static PyObject *__pyx_kp_s_105;
+static PyObject *__pyx_kp_s_106;
+static PyObject *__pyx_kp_u_107;
+static PyObject *__pyx_kp_u_108;
+static PyObject *__pyx_kp_u_109;
+static PyObject *__pyx_n_s_11;
+static PyObject *__pyx_kp_u_110;
+static PyObject *__pyx_kp_u_111;
+static PyObject *__pyx_kp_u_112;
+static PyObject *__pyx_kp_u_113;
+static PyObject *__pyx_kp_u_114;
+static PyObject *__pyx_kp_u_115;
+static PyObject *__pyx_kp_u_116;
+static PyObject *__pyx_kp_u_117;
+static PyObject *__pyx_kp_u_118;
+static PyObject *__pyx_kp_u_119;
+static PyObject *__pyx_kp_s_12;
+static PyObject *__pyx_kp_u_120;
+static PyObject *__pyx_kp_u_121;
+static PyObject *__pyx_kp_u_122;
+static PyObject *__pyx_kp_u_123;
+static PyObject *__pyx_kp_u_124;
+static PyObject *__pyx_kp_s_14;
+static PyObject *__pyx_kp_s_16;
+static PyObject *__pyx_n_s_17;
+static PyObject *__pyx_kp_s_18;
+static PyObject *__pyx_kp_s_19;
+static PyObject *__pyx_kp_s_2;
+static PyObject *__pyx_n_s_20;
+static PyObject *__pyx_n_s_21;
+static PyObject *__pyx_kp_s_22;
+static PyObject *__pyx_kp_s_23;
+static PyObject *__pyx_kp_s_24;
+static PyObject *__pyx_kp_s_25;
+static PyObject *__pyx_n_s_26;
+static PyObject *__pyx_kp_s_27;
+static PyObject *__pyx_kp_s_28;
+static PyObject *__pyx_kp_s_29;
+static PyObject *__pyx_kp_s_3;
+static PyObject *__pyx_kp_s_30;
+static PyObject *__pyx_kp_s_31;
+static PyObject *__pyx_kp_s_33;
+static PyObject *__pyx_kp_s_34;
+static PyObject *__pyx_kp_s_35;
+static PyObject *__pyx_kp_s_38;
+static PyObject *__pyx_kp_s_39;
+static PyObject *__pyx_kp_s_4;
+static PyObject *__pyx_kp_s_40;
+static PyObject *__pyx_kp_s_41;
+static PyObject *__pyx_kp_s_42;
+static PyObject *__pyx_kp_s_43;
+static PyObject *__pyx_kp_s_44;
+static PyObject *__pyx_kp_s_45;
+static PyObject *__pyx_kp_s_46;
+static PyObject *__pyx_n_s_47;
+static PyObject *__pyx_kp_s_48;
+static PyObject *__pyx_kp_s_49;
+static PyObject *__pyx_kp_s_5;
+static PyObject *__pyx_kp_s_50;
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+static PyObject *__pyx_n_s__GTstring;
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+static PyObject *__pyx_n_s__NT_PHASED_GENOTYPES;
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+static PyObject *__pyx_n_s__PASS;
+static PyObject *__pyx_n_s__POS;
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+static PyObject *__pyx_n_s__POS_NOT_POSITIVE;
+static PyObject *__pyx_n_s__QUAL;
+static PyObject *__pyx_n_s__QUAL_NOT_NUMERICAL;
+static PyObject *__pyx_n_s__REF;
+static PyObject *__pyx_n_s__StopIteration;
+static PyObject *__pyx_n_s__String;
+static PyObject *__pyx_n_s__Tabixfile;
+static PyObject *__pyx_n_s__Type;
+static PyObject *__pyx_n_s__UNKNOWN_CHAR_IN_REF;
+static PyObject *__pyx_n_s__V33_BAD_ALLELE;
+static PyObject *__pyx_n_s__V33_BAD_REF;
+static PyObject *__pyx_n_s__V40_BAD_ALLELE;
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+static PyObject *__pyx_n_s__VCFRecord;
+static PyObject *__pyx_n_s__ValueError;
+static PyObject *__pyx_n_s__WRONG_REF;
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+static PyObject *__pyx_n_s___lineno;
+static PyObject *__pyx_n_s___lines;
+static PyObject *__pyx_n_s___parse;
+static PyObject *__pyx_n_s___parse_header;
+static PyObject *__pyx_n_s___reference;
+static PyObject *__pyx_n_s___regions;
+static PyObject *__pyx_n_s___required;
+static PyObject *__pyx_n_s___sample2column;
+static PyObject *__pyx_n_s___samples;
+static PyObject *__pyx_n_s___version;
+static PyObject *__pyx_n_s___warn_errors;
+static PyObject *__pyx_n_s__add;
+static PyObject *__pyx_n_s__alleleRegEx;
+static PyObject *__pyx_n_s__alt;
+static PyObject *__pyx_n_s__alt1;
+static PyObject *__pyx_n_s__alt2;
+static PyObject *__pyx_n_s__bisect;
+static PyObject *__pyx_n_s__buffer;
+static PyObject *__pyx_n_s__chrom;
+static PyObject *__pyx_n_s__collections;
+static PyObject *__pyx_n_s__compare_calls;
+static PyObject *__pyx_n_s__compile;
+static PyObject *__pyx_n_s__connect;
+static PyObject *__pyx_n_s__contig;
+static PyObject *__pyx_n_s__convertGT;
+static PyObject *__pyx_n_s__convertGTback;
+static PyObject *__pyx_n_s__copy;
+static PyObject *__pyx_n_s__data;
+static PyObject *__pyx_n_s__datagenerator;
+static PyObject *__pyx_n_s__deepcopy;
+static PyObject *__pyx_n_s__defaultdict;
+static PyObject *__pyx_n_s__descr;
+static PyObject *__pyx_n_s__description;
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+static PyObject *__pyx_n_s__get;
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+static PyObject *__pyx_n_s__getfilter;
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+static PyObject *__pyx_n_s__getsamples;
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+static PyObject *__pyx_n_s__id;
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+static PyObject *__pyx_n_s__itemgetter;
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+static PyObject *__pyx_n_s__len;
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+static PyObject *__pyx_n_s__lines;
+static PyObject *__pyx_n_s__map;
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+static PyObject *__pyx_n_s__nfields;
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+static PyObject *__pyx_n_s__parse_formatdata;
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+static PyObject *__pyx_n_s__parse_heading;
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+static PyObject *__pyx_n_s__startswith;
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+static PyObject *__pyx_n_s__version;
+static PyObject *__pyx_n_s__warnerror;
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+static PyObject *__pyx_n_s__write_data;
+static PyObject *__pyx_n_s__write_header;
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+}
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+ #if PY_MAJOR_VERSION < 3
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+ __pyx_sq_item_4cvcf_VCFRecord, /*sq_item*/
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+}
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+}
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+}
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+ #endif
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+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
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+ 0, /*nb_inplace_divide*/
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+ 0, /*nb_inplace_lshift*/
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+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
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+
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+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
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+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
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+ #if PY_VERSION_HEX >= 0x02060000
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+ __pyx_tp_dealloc_4cvcf_asVCFRecord, /*tp_dealloc*/
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+ &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/
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+ 0, /*tp_str*/
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+ 0, /*tp_setattro*/
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+ 0, /*tp_mro*/
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+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
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+ {__Pyx_NAMESTR("parse_regions"), (PyCFunction)__pyx_pf_4cvcf_parse_regions, METH_O, __Pyx_DOCSTR(0)},
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+ NULL, /* m_clear */
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+ {&__pyx_n_s__setfilter, __pyx_k__setfilter, sizeof(__pyx_k__setfilter), 0, 0, 1, 1},
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+ {&__pyx_n_s__setheader, __pyx_k__setheader, sizeof(__pyx_k__setheader), 0, 0, 1, 1},
+ {&__pyx_n_s__setinfo, __pyx_k__setinfo, sizeof(__pyx_k__setinfo), 0, 0, 1, 1},
+ {&__pyx_n_s__setreference, __pyx_k__setreference, sizeof(__pyx_k__setreference), 0, 0, 1, 1},
+ {&__pyx_n_s__setregions, __pyx_k__setregions, sizeof(__pyx_k__setregions), 0, 0, 1, 1},
+ {&__pyx_n_s__setsamples, __pyx_k__setsamples, sizeof(__pyx_k__setsamples), 0, 0, 1, 1},
+ {&__pyx_n_s__setversion, __pyx_k__setversion, sizeof(__pyx_k__setversion), 0, 0, 1, 1},
+ {&__pyx_n_s__split, __pyx_k__split, sizeof(__pyx_k__split), 0, 0, 1, 1},
+ {&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1},
+ {&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1},
+ {&__pyx_n_s__stderr, __pyx_k__stderr, sizeof(__pyx_k__stderr), 0, 0, 1, 1},
+ {&__pyx_n_s__stream, __pyx_k__stream, sizeof(__pyx_k__stream), 0, 0, 1, 1},
+ {&__pyx_n_s__strip, __pyx_k__strip, sizeof(__pyx_k__strip), 0, 0, 1, 1},
+ {&__pyx_n_s__sys, __pyx_k__sys, sizeof(__pyx_k__sys), 0, 0, 1, 1},
+ {&__pyx_n_s__tabixfile, __pyx_k__tabixfile, sizeof(__pyx_k__tabixfile), 0, 0, 1, 1},
+ {&__pyx_n_s__type, __pyx_k__type, sizeof(__pyx_k__type), 0, 0, 1, 1},
+ {&__pyx_n_s__upper, __pyx_k__upper, sizeof(__pyx_k__upper), 0, 0, 1, 1},
+ {&__pyx_n_s__validate, __pyx_k__validate, sizeof(__pyx_k__validate), 0, 0, 1, 1},
+ {&__pyx_n_s__value, __pyx_k__value, sizeof(__pyx_k__value), 0, 0, 1, 1},
+ {&__pyx_n_s__vcf, __pyx_k__vcf, sizeof(__pyx_k__vcf), 0, 0, 1, 1},
+ {&__pyx_n_s__vcffile, __pyx_k__vcffile, sizeof(__pyx_k__vcffile), 0, 0, 1, 1},
+ {&__pyx_n_s__version, __pyx_k__version, sizeof(__pyx_k__version), 0, 0, 1, 1},
+ {&__pyx_n_s__warnerror, __pyx_k__warnerror, sizeof(__pyx_k__warnerror), 0, 0, 1, 1},
+ {&__pyx_n_s__write, __pyx_k__write, sizeof(__pyx_k__write), 0, 0, 1, 1},
+ {&__pyx_n_s__write_data, __pyx_k__write_data, sizeof(__pyx_k__write_data), 0, 0, 1, 1},
+ {&__pyx_n_s__write_header, __pyx_k__write_header, sizeof(__pyx_k__write_header), 0, 0, 1, 1},
+ {&__pyx_n_s__write_heading, __pyx_k__write_heading, sizeof(__pyx_k__write_heading), 0, 0, 1, 1},
+ {&__pyx_n_s__writeheader, __pyx_k__writeheader, sizeof(__pyx_k__writeheader), 0, 0, 1, 1},
+ {&__pyx_n_s__zip, __pyx_k__zip, sizeof(__pyx_k__zip), 0, 0, 1, 1},
+ {0, 0, 0, 0, 0, 0, 0}
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+PyMODINIT_FUNC initcvcf(void); /*proto*/
+PyMODINIT_FUNC initcvcf(void)
+#else
+PyMODINIT_FUNC PyInit_cvcf(void); /*proto*/
+PyMODINIT_FUNC PyInit_cvcf(void)
+#endif
+{
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+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
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+ void* __pyx_refnanny = NULL;
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+ __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny");
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+ __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #ifdef __pyx_binding_PyCFunctionType_USED
+ if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ /*--- Library function declarations ---*/
+ /*--- Threads initialization code ---*/
+ #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS
+ #ifdef WITH_THREAD /* Python build with threading support? */
+ PyEval_InitThreads();
+ #endif
+ #endif
+ /*--- Module creation code ---*/
+ #if PY_MAJOR_VERSION < 3
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
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+ __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);
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+ 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;}
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+ }
+ /*--- Builtin init code ---*/
+ if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Global init 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;}
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+ #else
+ *(void(**)(void))&__pyx_vtable_4cvcf_VCFRecord.__pyx_base.update = (void(*)(void))__pyx_f_4cvcf_9VCFRecord_update;
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+ __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_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;}
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+ __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 = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict, &__pyx_vtabptr_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ /*--- Function import code ---*/
+ /*--- Execution code ---*/
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+ * from collections import namedtuple, defaultdict # <<<<<<<<<<<<<<
+ * from operator import itemgetter
+ * import sys, re, copy, bisect
+ */
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+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__namedtuple));
+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__namedtuple));
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+ * cdef extern from "string.h": # <<<<<<<<<<<<<<
+ * ctypedef int size_t
+ * void *memcpy(void *dst,void *src,size_t len)
+ */
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_3);
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+ if (__pyx_m) {
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+ return;
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+ return __pyx_m;
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+}
+
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+
+static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
+ PyObject *result;
+ result = PyObject_GetAttr(dict, name);
+ if (!result)
+ PyErr_SetObject(PyExc_NameError, name);
+ return result;
+}
+
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%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));
+ #endif
+}
+
+static void __Pyx_RaiseArgtupleInvalid(
+ const char* func_name,
+ int exact,
+ Py_ssize_t num_min,
+ Py_ssize_t num_max,
+ Py_ssize_t num_found)
+{
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+
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+ } else {
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+ more_or_less = "at most";
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+ }
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+ PyErr_Format(PyExc_TypeError,
+ #if PY_VERSION_HEX < 0x02050000
+ "%s() takes %s %d positional argument%s (%d given)",
+ #else
+ "%s() takes %s %zd positional argument%s (%zd given)",
+ #endif
+ func_name, more_or_less, num_expected, number, num_found);
+}
+
+static int __Pyx_ParseOptionalKeywords(
+ PyObject *kwds,
+ PyObject **argnames[],
+ PyObject *kwds2,
+ PyObject *values[],
+ Py_ssize_t num_pos_args,
+ const char* function_name)
+{
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+ Py_ssize_t pos = 0;
+ PyObject*** name;
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+
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+ #if PY_MAJOR_VERSION >= 3
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+ }
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+ } else {
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+ }
+ }
+ }
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%s() keywords must be strings", function_name);
+ goto bad;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%s() got an unexpected keyword argument '%s'",
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+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
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+}
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+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
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+ if (unlikely(tstate->curexc_type))
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
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+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
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+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
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+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+ return 0;
+bad:
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+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
+
+static double __Pyx__PyObject_AsDouble(PyObject* obj) {
+ PyObject* float_value;
+ 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)) {
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+ float_value = PyFloat_FromString(obj);
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+ float_value = PyFloat_FromString(obj, 0);
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+ } else {
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+ }
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+ Py_DECREF(float_value);
+ return value;
+ }
+bad:
+ return (double)-1;
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
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+ #else
+ "need more than %zd value%s to unpack", index,
+ #endif
+ (index == 1) ? "" : "s");
+}
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+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ #if PY_VERSION_HEX < 0x02050000
+ "too many values to unpack (expected %d)", (int)expected);
+ #else
+ "too many values to unpack (expected %zd)", expected);
+ #endif
+}
+
+static PyObject *__Pyx_UnpackItem(PyObject *iter, Py_ssize_t index) {
+ PyObject *item;
+ if (!(item = PyIter_Next(iter))) {
+ if (!PyErr_Occurred()) {
+ __Pyx_RaiseNeedMoreValuesError(index);
+ }
+ }
+ return item;
+}
+
+static int __Pyx_EndUnpack(PyObject *iter, Py_ssize_t expected) {
+ PyObject *item;
+ if ((item = PyIter_Next(iter))) {
+ Py_DECREF(item);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ }
+ else if (!PyErr_Occurred())
+ return 0;
+ else
+ return -1;
+}
+
+static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) {
+ Py_ssize_t q = a / b;
+ Py_ssize_t r = a - q*b;
+ q -= ((r != 0) & ((r ^ b) < 0));
+ return q;
+}
+
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->exc_type;
+ *value = tstate->exc_value;
+ *tb = tstate->exc_traceback;
+ Py_XINCREF(*type);
+ Py_XINCREF(*value);
+ Py_XINCREF(*tb);
+}
+
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = type;
+ tstate->exc_value = value;
+ tstate->exc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list) {
+ PyObject *py_import = 0;
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
+ if (!py_import)
+ goto bad;
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, NULL);
+bad:
+ Py_XDECREF(empty_list);
+ Py_XDECREF(py_import);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+static PyObject *__Pyx_CreateClass(
+ PyObject *bases, PyObject *dict, PyObject *name, const char *modname)
+{
+ PyObject *py_modname;
+ PyObject *result = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_modname = PyString_FromString(modname);
+ #else
+ py_modname = PyUnicode_FromString(modname);
+ #endif
+ if (!py_modname)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__module__", py_modname) < 0)
+ goto bad;
+ #if PY_MAJOR_VERSION < 3
+ result = PyClass_New(bases, dict, name);
+ #else
+ result = PyObject_CallFunctionObjArgs((PyObject *)&PyType_Type, name, bases, dict, NULL);
+ #endif
+bad:
+ Py_XDECREF(py_modname);
+ return result;
+}
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+}
+
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+}
+
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ Py_XINCREF(type);
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ 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;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
+ Py_INCREF(value);
+ }
+ #if PY_VERSION_HEX < 0x02050000
+ if (!PyClass_Check(type))
+ #else
+ if (!PyType_Check(type))
+ #endif
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
+ value = type;
+ #if PY_VERSION_HEX < 0x02050000
+ if (PyInstance_Check(type)) {
+ type = (PyObject*) ((PyInstanceObject*)type)->in_class;
+ Py_INCREF(type);
+ }
+ else {
+ type = 0;
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception must be an old-style class or instance");
+ goto raise_error;
+ }
+ #else
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ #endif
+ }
+
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+
+#else /* Python 3+ */
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb) {
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (!PyExceptionClass_Check(type)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+
+ PyErr_SetObject(type, value);
+
+ if (tb) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+ }
+
+bad:
+ return;
+}
+#endif
+
+static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
+ const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if ((sizeof(uint32_t) == sizeof(char)) ||
+ (sizeof(uint32_t) == sizeof(short))) {
+ return PyInt_FromLong((long)val);
+ } else if ((sizeof(uint32_t) == sizeof(int)) ||
+ (sizeof(uint32_t) == sizeof(long))) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLong((unsigned long)val);
+ else
+ return PyInt_FromLong((long)val);
+ } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val);
+ else
+ return PyLong_FromLongLong((PY_LONG_LONG)val);
+ } else {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
+ little, !is_unsigned);
+ }
+}
+
+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;
+ if (sizeof(unsigned char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned char" :
+ "value too large to convert to unsigned char");
+ }
+ return (unsigned char)-1;
+ }
+ return (unsigned char)val;
+ }
+ return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) {
+ const unsigned short neg_one = (unsigned short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned short" :
+ "value too large to convert to unsigned short");
+ }
+ return (unsigned short)-1;
+ }
+ return (unsigned short)val;
+ }
+ return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) {
+ const unsigned int neg_one = (unsigned int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(unsigned int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(unsigned int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to unsigned int" :
+ "value too large to convert to unsigned int");
+ }
+ return (unsigned int)-1;
+ }
+ return (unsigned int)val;
+ }
+ return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x);
+}
+
+static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) {
+ const char neg_one = (char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to char" :
+ "value too large to convert to char");
+ }
+ return (char)-1;
+ }
+ return (char)val;
+ }
+ return (char)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) {
+ const short neg_one = (short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to short" :
+ "value too large to convert to short");
+ }
+ return (short)-1;
+ }
+ return (short)val;
+ }
+ return (short)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) {
+ const signed char neg_one = (signed char)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed char) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed char)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed char" :
+ "value too large to convert to signed char");
+ }
+ return (signed char)-1;
+ }
+ return (signed char)val;
+ }
+ return (signed char)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) {
+ const signed short neg_one = (signed short)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed short) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed short)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed short" :
+ "value too large to convert to signed short");
+ }
+ return (signed short)-1;
+ }
+ return (signed short)val;
+ }
+ return (signed short)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) {
+ const signed int neg_one = (signed int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(signed int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(signed int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to signed int" :
+ "value too large to convert to signed int");
+ }
+ return (signed int)-1;
+ }
+ return (signed int)val;
+ }
+ return (signed int)__Pyx_PyInt_AsSignedLong(x);
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) {
+ const int neg_one = (int)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (sizeof(int) < sizeof(long)) {
+ long val = __Pyx_PyInt_AsLong(x);
+ if (unlikely(val != (long)(int)val)) {
+ if (!unlikely(val == -1 && PyErr_Occurred())) {
+ PyErr_SetString(PyExc_OverflowError,
+ (is_unsigned && unlikely(val < 0)) ?
+ "can't convert negative value to int" :
+ "value too large to convert to int");
+ }
+ return (int)-1;
+ }
+ return (int)val;
+ }
+ return (int)__Pyx_PyInt_AsLong(x);
+}
+
+static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) {
+ const unsigned long neg_one = (unsigned long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return (unsigned long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned long");
+ return (unsigned long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ unsigned long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned long)-1;
+ val = __Pyx_PyInt_AsUnsignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) {
+ const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return (unsigned PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to unsigned PY_LONG_LONG");
+ return (unsigned PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ unsigned PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (unsigned PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsUnsignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) {
+ const long neg_one = (long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return (long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long)-1;
+ val = __Pyx_PyInt_AsLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) {
+ const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return (PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to PY_LONG_LONG");
+ return (PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) {
+ const signed long neg_one = (signed long)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
+ }
+ return (signed long)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed long");
+ return (signed long)-1;
+ }
+ return PyLong_AsUnsignedLong(x);
+ } else {
+ return PyLong_AsLong(x);
+ }
+ } else {
+ signed long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed long)-1;
+ val = __Pyx_PyInt_AsSignedLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
+ const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_VERSION_HEX < 0x03000000
+ if (likely(PyInt_Check(x))) {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return (signed PY_LONG_LONG)val;
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+ if (unlikely(Py_SIZE(x) < 0)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to signed PY_LONG_LONG");
+ return (signed PY_LONG_LONG)-1;
+ }
+ return PyLong_AsUnsignedLongLong(x);
+ } else {
+ return PyLong_AsLongLong(x);
+ }
+ } else {
+ signed PY_LONG_LONG val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (signed PY_LONG_LONG)-1;
+ val = __Pyx_PyInt_AsSignedLongLong(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+}
+
+#ifndef __PYX_HAVE_RT_ImportType
+#define __PYX_HAVE_RT_ImportType
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
+ long size, int strict)
+{
+ PyObject *py_module = 0;
+ PyObject *result = 0;
+ PyObject *py_name = 0;
+ char warning[200];
+
+ py_module = __Pyx_ImportModule(module_name);
+ if (!py_module)
+ goto bad;
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(class_name);
+ #else
+ py_name = PyUnicode_FromString(class_name);
+ #endif
+ if (!py_name)
+ goto bad;
+ result = PyObject_GetAttr(py_module, py_name);
+ Py_DECREF(py_name);
+ py_name = 0;
+ Py_DECREF(py_module);
+ py_module = 0;
+ if (!result)
+ goto bad;
+ if (!PyType_Check(result)) {
+ PyErr_Format(PyExc_TypeError,
+ "%s.%s is not a type object",
+ module_name, class_name);
+ goto bad;
+ }
+ if (!strict && ((PyTypeObject *)result)->tp_basicsize > size) {
+ PyOS_snprintf(warning, sizeof(warning),
+ "%s.%s size changed, may indicate binary incompatibility",
+ module_name, class_name);
+ #if PY_VERSION_HEX < 0x02050000
+ PyErr_Warn(NULL, warning);
+ #else
+ PyErr_WarnEx(NULL, warning, 0);
+ #endif
+ }
+ else if (((PyTypeObject *)result)->tp_basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%s.%s has the wrong size, try recompiling",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_module);
+ Py_XDECREF(result);
+ return 0;
+}
+#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;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ 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 int __Pyx_GetVtable(PyObject *dict, void *vtabptr) {
+ PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
+ if (!ob)
+ goto bad;
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ *(void **)vtabptr = PyCapsule_GetPointer(ob, 0);
+#else
+ *(void **)vtabptr = PyCObject_AsVoidPtr(ob);
+#endif
+ if (!*(void **)vtabptr)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+
+static void __Pyx_AddTraceback(const char *funcname) {
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(__pyx_filename);
+ #else
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (__pyx_clineno) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_code = PyCode_New(
+ 0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
+ 0, /*int kwonlyargcount,*/
+ #endif
+ 0, /*int nlocals,*/
+ 0, /*int stacksize,*/
+ 0, /*int flags,*/
+ __pyx_empty_bytes, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ __pyx_lineno, /*int firstlineno,*/
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ if (!py_code) goto bad;
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ py_globals, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = __pyx_lineno;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ while (t->p) {
+ #if PY_MAJOR_VERSION < 3
+ if (t->is_unicode) {
+ *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+ } else if (t->intern) {
+ *t->p = PyString_InternFromString(t->s);
+ } else {
+ *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+ }
+ #else /* Python 3+ has unicode identifiers */
+ if (t->is_unicode | t->is_str) {
+ if (t->intern) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->encoding) {
+ *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
+ } else {
+ *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+ }
+ } else {
+ *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+ }
+ #endif
+ if (!*t->p)
+ return -1;
+ ++t;
+ }
+ return 0;
+}
+
+/* Type Conversion Functions */
+
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+ int is_true = x == Py_True;
+ if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
+ else return PyObject_IsTrue(x);
+}
+
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
+ PyNumberMethods *m;
+ const char *name = NULL;
+ PyObject *res = NULL;
+#if PY_VERSION_HEX < 0x03000000
+ if (PyInt_Check(x) || PyLong_Check(x))
+#else
+ if (PyLong_Check(x))
+#endif
+ return Py_INCREF(x), x;
+ m = Py_TYPE(x)->tp_as_number;
+#if PY_VERSION_HEX < 0x03000000
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Int(x);
+ }
+ else if (m && m->nb_long) {
+ name = "long";
+ res = PyNumber_Long(x);
+ }
+#else
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Long(x);
+ }
+#endif
+ if (res) {
+#if PY_VERSION_HEX < 0x03000000
+ if (!PyInt_Check(res) && !PyLong_Check(res)) {
+#else
+ if (!PyLong_Check(res)) {
+#endif
+ PyErr_Format(PyExc_TypeError,
+ "__%s__ returned non-%s (type %.200s)",
+ name, name, Py_TYPE(res)->tp_name);
+ Py_DECREF(res);
+ return NULL;
+ }
+ }
+ else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_TypeError,
+ "an integer is required");
+ }
+ return res;
+}
+
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
+ Py_ssize_t ival;
+ PyObject* x = PyNumber_Index(b);
+ if (!x) return -1;
+ ival = PyInt_AsSsize_t(x);
+ Py_DECREF(x);
+ return ival;
+}
+
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
+#if PY_VERSION_HEX < 0x02050000
+ if (ival <= LONG_MAX)
+ return PyInt_FromLong((long)ival);
+ else {
+ unsigned char *bytes = (unsigned char *) &ival;
+ int one = 1; int little = (int)*(unsigned char*)&one;
+ return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
+ }
+#else
+ return PyInt_FromSize_t(ival);
+#endif
+}
+
+static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
+ unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
+ if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
+ return (size_t)-1;
+ } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) {
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t)-1;
+ }
+ return (size_t)val;
+}
+
+
+#endif /* Py_PYTHON_H */
--- /dev/null
+cdef extern from "stdlib.h":
+ void free(void *)
+ void *malloc(size_t)
+ void *calloc(size_t,size_t)
+ void *realloc(void *,size_t)
+ int c_abs "abs" (int)
+ int c_abs "abs" (int)
+ int atoi( char *nptr)
+ long atol( char *nptr)
+ double atof( char *nptr)
+
+cdef extern from "Python.h":
+ ctypedef struct FILE
+ FILE* PyFile_AsFile(object)
+ char *fgets(char *str, int size, FILE *ifile)
+ int feof(FILE *stream)
+ size_t strlen(char *s)
+ size_t getline(char **lineptr, size_t *n, FILE *stream)
+ char *strstr(char *, char *)
+ char *strchr(char *string, int c)
+ int fileno(FILE *stream)
+
+cdef extern from "string.h":
+ int strcmp(char *s1, char *s2)
+ int strncmp(char *s1,char *s2,size_t len)
+ char *strcpy(char *dest,char *src)
+ char *strncpy(char *dest,char *src, size_t len)
+ char *strdup(char *)
+ char *strcat(char *,char *)
+ size_t strlen(char *s)
+ int memcmp( void * s1, void *s2, size_t len )
+ void *memcpy(void *dest, void *src, size_t n)
+ void *memchr(void *s, int c, size_t n)
+
+cdef extern from "stdint.h":
+ ctypedef int int64_t
+ ctypedef int int32_t
+ ctypedef int uint32_t
+ ctypedef int uint8_t
+ ctypedef int uint64_t
+
--- /dev/null
+#
+# Code to read, write and edit VCF files
+#
+# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
+# 'chrom': string
+# 'pos': integer
+# 'id': string
+# 'ref': string
+# 'alt': list of strings
+# 'qual': integer
+# 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
+# 'info': dictionary of values (see below)
+# 'format': list of keys (strings)
+# sample keys: dictionary of values (see below)
+#
+# The sample keys are accessible through vcf.getsamples()
+#
+# A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map
+# to a list, containign integers, floats, strings, or characters. Missing values are replaced
+# by a particular value, often -1 or .
+#
+# Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples),
+# the first (and last) the integer representing an allele, and the second the separation character.
+# Note that there is just one genotype per sample, but for consistency the single element is stored in a list.
+#
+# Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible
+# through getheader()
+#
+# The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding
+# 0-based half-open segments. Only variants with a position inside the segment will be parsed. A regions
+# parser is available under parse_regions.
+#
+# When instantiated, a reference can be passed to the VCF class. This may be any class that supports a
+# fetch(chrom, start, end) method.
+#
+#
+#
+# NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file.
+#
+#
+#
+# TODO:
+# only v4.0 writing is complete; alleles are not converted to v3.3 format
+#
+
+from collections import namedtuple, defaultdict
+from operator import itemgetter
+import sys, re, copy, bisect
+
+cimport ctabix
+cimport TabProxies
+import pysam
+
+gtsRegEx = re.compile("[|/\\\\]")
+alleleRegEx = re.compile('^[ACGTN]+$')
+
+# Utility function. Uses 0-based coordinates
+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()
+ sequence = fa.fetch(chrom, start, end).upper()
+ if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
+ return sequence
+
+# Utility function. Parses a region string
+def parse_regions( string ):
+ result = []
+ for r in string.split(','):
+ elts = r.split(':')
+ chrom, start, end = elts[0], 0, 3000000000
+ if len(elts)==1: pass
+ elif len(elts)==2:
+ if len(elts[1])>0:
+ 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])
+ except: raise ValueError("Don't understand region string '%s'" % r)
+ else:
+ raise ValueError("Don't understand region string '%s'" % r)
+ result.append( (chrom,start,end) )
+ return result
+
+
+FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
+
+###########################################################################################################
+#
+# New class
+#
+###########################################################################################################
+
+cdef class VCFRecord( TabProxies.TupleProxy):
+ '''vcf record.
+
+ initialized from data and vcf meta
+ '''
+
+ cdef vcf
+ cdef char * contig
+ cdef uint32_t pos
+
+ def __init__(self, vcf):
+ self.vcf = vcf
+ # if len(data) != len(self.vcf._samples):
+ # self.error(str(data),
+ # self.BAD_NUMBER_OF_COLUMNS,
+ # "expected %s for %s samples (%s), got %s" % \
+ # (len(self.vcf._samples),
+ # len(self.vcf._samples),
+ # self.vcf._samples,
+ # len(data)))
+
+ def __cinit__(self, vcf ):
+ # start indexed access at genotypes
+ self.offset = 9
+
+ self.vcf = vcf
+
+ cdef update( self, char * buffer, size_t nbytes ):
+ '''update internal data.
+
+ nbytes does not include the terminal '\0'.
+ '''
+ TabProxies.TupleProxy.update( self, buffer, nbytes )
+
+ self.contig = self.fields[0]
+ # vcf counts from 1 - correct here
+ self.pos = atoi( self.fields[1] ) - 1
+
+ def __len__(self):
+ return max(0, self.nfields - 9)
+
+ property contig:
+ def __get__(self): return self.contig
+
+ property pos:
+ def __get__(self): return self.pos
+
+ property id:
+ def __get__(self): return self.fields[2]
+
+ property ref:
+ def __get__(self): return self.fields[3]
+
+ property alt:
+ def __get__(self):
+ # convert v3.3 to v4.0 alleles below
+ alt = self.fields[4]
+ if alt == ".": alt = []
+ else: alt = alt.upper().split(',')
+ return alt
+
+ property qual:
+ def __get__(self):
+ qual = self.fields[5]
+ if qual == b".": qual = -1
+ else:
+ try: qual = float(qual)
+ except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
+
+ property filter:
+ def __get__(self):
+ 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 []
+ else: return f.split(';')
+
+ property info:
+ def __get__(self):
+ col = self.fields[7]
+ # dictionary of keys, and list of values
+ info = {}
+ if col != b".":
+ for blurp in col.split(';'):
+ elts = blurp.split('=')
+ if len(elts) == 1: v = None
+ 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))
+ return info
+
+ property format:
+ def __get__(self):
+ return self.fields[8].split(':')
+
+ property samples:
+ def __get__(self):
+ return self.vcf._samples
+
+ def __getitem__(self, key):
+
+ # parse sample columns
+ values = self.fields[self.vcf._sample2column[key]].split(':')
+ alt = self.alt
+ format = self.format
+
+ 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)))
+
+ result = {}
+ for idx in range(len(format)):
+ expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
+ if idx < len(values): value = values[idx]
+ else:
+ if expected == -1: value = "."
+ else: value = ",".join(["."]*expected)
+
+ 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]]))
+ 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]
+
+ return result
+
+
+cdef class asVCFRecord( ctabix.Parser ):
+ '''converts a :term:`tabix row` into a VCF record.'''
+ cdef vcffile
+ def __init__(self, vcffile ):
+ self.vcffile = vcffile
+ def __call__(self, char * buffer, int len ):
+ cdef VCFRecord r
+ r = VCFRecord( self.vcffile )
+ r.copy( buffer, len )
+ return r
+
+class VCF(object):
+
+ # types
+ NT_UNKNOWN = 0
+ NT_NUMBER = 1
+ NT_ALLELES = 2
+ NT_NR_ALLELES = 3
+ NT_GENOTYPES = 4
+ NT_PHASED_GENOTYPES = 5
+
+ _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
+ 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
+ 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
+ 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
+ 4:"POS_NOT_NUMERICAL:Position column is not numerical",
+ 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
+ 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
+ 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
+ 8:"POS_NOT_POSITIVE:Position field must be >0",
+ 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
+ 10:"ERROR_INFO_STRING:Error while parsing info field",
+ 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
+ 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
+ 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
+ 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
+ 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
+ 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
+ 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
+ 18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
+ 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
+ 20:"MISSING_REF:Reference allele missing",
+ 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
+ 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
+ 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
+ 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
+ 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
+ 26:"WRONG_REF:Wrong reference %s",
+ 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
+ 28:"BAD_CHR_TAG:Error calculating chr tag for %s",
+ 29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
+ 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"
+ }
+
+ # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
+ _header = []
+
+ # version number; 33=v3.3; 40=v4.0
+ _version = 40
+
+ # info, filter and format data
+ _info = {}
+ _filter = {}
+ _format = {}
+
+ # header; and required columns
+ _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
+ _samples = []
+
+ # control behaviour
+ _ignored_errors = set([11]) # ERROR_UNKNOWN_KEY
+ _warn_errors = set([])
+ _leftalign = False
+
+ # reference sequence
+ _reference = None
+
+ # regions to include; None includes everything
+ _regions = None
+
+ # statefull stuff
+ _lineno = -1
+ _line = None
+ _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
+ if _copy != None:
+ self._leftalign = _copy._leftalign
+ self._header = _copy._header[:]
+ self._version = _copy._version
+ self._info = copy.deepcopy(_copy._info)
+ self._filter = copy.deepcopy(_copy._filter)
+ self._format = copy.deepcopy(_copy._format)
+ self._samples = _copy._samples[:]
+ self._sample2column = copy.deepcopy(_copy._sample2column)
+ self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
+ self._warn_errors = copy.deepcopy(_copy._warn_errors)
+ self._reference = _copy._reference
+ self._regions = _copy._regions
+ if reference: self._reference = reference
+ if regions: self._regions = regions
+ if leftalign: self._leftalign = leftalign
+ self._lines = lines
+
+ def error(self,line,error,opt=None):
+ if error in self._ignored_errors: return
+ errorlabel, errorstring = self._errors[error].split(':')
+ if opt: errorstring = errorstring % opt
+ errwarn = ["Error","Warning"][error in self._warn_errors]
+ sys.stderr.write("Line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring))
+ if error in self._warn_errors: return
+ raise ValueError(errorstring)
+
+ def parse_format(self,line,format,filter=False):
+ if self._version == 40:
+ if not format.startswith('<'):
+ self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+ format = "<"+format
+ if not format.endswith('>'):
+ self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+ format += ">"
+ format = format[1:-1]
+ data = {'id':None,'number':None,'type':None,'descr':None}
+ idx = 0
+ while len(format.strip())>0:
+ elts = format.strip().split(',')
+ 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)
+ 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]
+ elif first.startswith('Number='): data['number'] = first.split('=')[1]
+ elif first.startswith('Type='): data['type'] = first.split('=')[1]
+ elif first.startswith('Description='):
+ elts = format.split('"')
+ if len(elts)<3:
+ self.error(line,self.FORMAT_MISSING_QUOTES)
+ elts = first.split('=') + [rest]
+ data['descr'] = elts[1]
+ rest = '"'.join(elts[2:])
+ if rest.startswith(','): rest = rest[1:]
+ else:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ format = rest
+ 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)
+ if not data['descr']:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ data['descr'] = '<none>'
+ if not data['type'] and not data['number']:
+ # fine, ##filter format
+ 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)
+ # 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'] = '.'
+ if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ try:
+ n = int(data['number'])
+ t = self.NT_NUMBER
+ except ValueError:
+ 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
+ elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
+ else:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ 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:
+ 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"
+ 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"
+ else:
+ raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
+ values.append( ('Number',nmb) )
+ values.append( ('Type', fmt.type) )
+ values.append( ('Description', '"' + fmt.description + '"') )
+ if self._version == 33:
+ format = ",".join([v for k,v in values])
+ else:
+ format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
+ return format
+
+ def get_expected(self, format, formatdict, alt):
+ fmt = formatdict[format]
+ 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
+ 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)
+ return 0
+
+
+ def _add_definition(self, formatdict, key, data, line ):
+ 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
+ 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)
+ return
+ if type(data[0]) == type(0):
+ formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
+ return
+ formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
+
+
+ # 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
+ d = {}
+ for k in data: d[k] = []
+ data = d
+ # convert missing values; and silently add definitions if required
+ for k in data:
+ self._add_definition( format, k, data[k], "(output)" )
+ for idx,v in enumerate(data[k]):
+ 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:
+ 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:
+ 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)
+ elif value:
+ if v != None: output.append( ','.join(map(str,v)) )
+ else: output.append( "." ) # should not happen
+ # snip off trailing missing data
+ while len(output) > 1:
+ last = output[-1].replace(',','').replace('.','')
+ if len(last)>0: break
+ output = output[:-1]
+ return separator.join(output)
+
+
+ def enter_default_format(self):
+ for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
+ FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
+ FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
+ FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
+ FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.')]:
+ if f.id not in self._format:
+ self._format[f.id] = f
+
+ def parse_header( self, line ):
+ assert line.startswith('##')
+ elts = line[2:].split('=')
+ key = elts[0].strip()
+ value = '='.join(elts[1:]).strip()
+ if key == "fileformat":
+ if value == "VCFv3.3":
+ self._version = 33
+ elif value == "VCFv4.0":
+ self._version = 40
+ elif value == "VCFv4.1":
+ # AH - for testing
+ self._version = 40
+ else:
+ self.error(line,self.UNKNOWN_FORMAT_STRING)
+ elif key == "INFO":
+ 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
+ elif key == "FORMAT":
+ f = self.parse_format(line, value)
+ self._format[ f.id ] = f
+ else:
+ # keep other keys in the header field
+ self._header.append( (key,value) )
+
+
+ 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))
+ 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"))))
+
+
+ def parse_heading( self, line ):
+ assert line.startswith('#')
+ assert not line.startswith('##')
+ headings = line[1:].split('\t')
+ if len(headings)==1 and len(line[1:].split()) >= 9:
+ self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
+ headings = line[1:].split()
+
+ for i,s in enumerate(self._required):
+
+ if len(headings)<=i or headings[i] != s:
+
+ if len(headings) <= i:
+ err = "(%sth entry not found)" % (i+1)
+ else:
+ err = "(found %s, expected %s)" % (headings[i],s)
+
+ #self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+ # allow FORMAT column to be absent
+ if len(headings) == 8:
+ headings.append("FORMAT")
+ else:
+ self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+ self._samples = headings[9:]
+ 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")
+
+ def convertGT(self, GTstring):
+ if GTstring == ".": return ["."]
+ try:
+ gts = gtsRegEx.split(GTstring)
+ 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:
+ self.error(self._line,self.BAD_GENOTYPE,GTstring)
+ return [".","|","."]
+
+
+ def convertGTback(self, GTdata):
+ 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)
+ if f == None:
+ self._add_definition(formatdict, key, value, line )
+ f = formatdict[key]
+ if f.type == "Flag":
+ 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:
+ 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):
+ try:
+ if v == ".": values[idx] = f.missingvalue
+ else: values[idx] = int(v)
+ except:
+ self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+ return [0] * len(values)
+ return values
+ elif f.type == "String":
+ self._line = line
+ if f.id == "GT": values = 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)
+ return values
+ elif f.type == "Float":
+ for idx,v in enumerate(values):
+ if v == ".": values[idx] = f.missingvalue
+ try: return map(float,values)
+ except:
+ self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+ return [0.0] * len(values)
+ else:
+ # can't happen
+ self.error(line,self.ERROR_INFO_STRING)
+
+
+ def inregion(self, chrom, pos):
+ if not self._regions: return True
+ for r in self._regions:
+ if r[0] == chrom and r[1] <= pos < r[2]: return True
+ return False
+
+
+ def parse_data( self, line, lineparse=False ):
+ cols = line.split('\t')
+ if len(cols) != len(self._samples)+9:
+ # gracefully deal with absent FORMAT column
+ if len(cols) == 8 and len(self._samples)==0:
+ cols.append("")
+ else:
+ 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)))
+
+ chrom = cols[0]
+
+ # get 0-based position
+ try: pos = int(cols[1])-1
+ except: self.error(line,self.POS_NOT_NUMERICAL)
+ if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
+
+ # implement filtering
+ if not self.inregion(chrom,pos): return None
+
+ # end of first-pass parse for sortedVCF
+ if lineparse: return chrom, pos, line
+
+ id = cols[2]
+
+ 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)
+ else: ref = ""
+ 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)
+
+ # make sure reference is sane
+ 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))
+ ref = faref
+
+ # convert v3.3 to v4.0 alleles below
+ if cols[4] == ".": alt = []
+ else: alt = cols[4].upper().split(',')
+
+ if cols[5] == ".": qual = -1
+ else:
+ try: qual = float(cols[5])
+ except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+ # 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(';')
+
+ # dictionary of keys, and list of values
+ info = {}
+ 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]
+ else: self.error(line,self.ERROR_INFO_STRING)
+ info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line)
+
+ # Gracefully deal with absent FORMAT column
+ if cols[8] == "": format = []
+ else: format = cols[8].split(':')
+
+ # 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
+ for f in format:
+ if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
+
+ # convert v3.3 alleles
+ if self._version == 33:
+ if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+ newalts = []
+ have_deletions = False
+ 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<seq> and D<num>
+ 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)
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ 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)
+ 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
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ a = ref[len(s):] # new deletion, deleting from pos
+ else:
+ self.error(line,self.V33_BAD_ALLELE)
+ newalts.append(a)
+ alt = newalts
+ # 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)
+ ref += addn
+ 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]
+ pos -= 1
+ else:
+ # format v4.0 -- just check for nucleotides
+ for allele in alt:
+ if not alleleRegEx.match(allele):
+ self.error(line,self.V40_BAD_ALLELE,allele)
+
+ # check for leading nucleotide in indel calls
+ for allele in alt:
+ 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)
+
+ # trim trailing bases in alleles
+ 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]
+
+ # left-align alleles, if a reference is available
+ if self._leftalign and self._reference:
+ while left < pos:
+ movable = True
+ for allele in alt:
+ if len(allele) > len(ref):
+ longest, shortest = allele, ref
+ else:
+ longest, shortest = ref, allele
+ 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:
+ 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
+ alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+ pos -= 1
+
+ # parse sample columns
+ samples = []
+ 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)))
+ for idx in range(len(format)):
+ expected = self.get_expected(format[idx], self._format, alt)
+ if idx < len(values): value = values[idx]
+ else:
+ if expected == -1: value = "."
+ else: value = ",".join(["."]*expected)
+ dict[format[idx]] = self.parse_formatdata(format[idx], value, 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]]))
+ 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 )
+
+ # done
+ d = {'chrom':chrom,
+ 'pos':pos, # return 0-based position
+ 'id':id,
+ 'ref':ref,
+ 'alt':alt,
+ 'qual':qual,
+ 'filter':filter,
+ 'info':info,
+ 'format':format}
+ for key,value in zip(self._samples,samples):
+ d[key] = value
+
+ return d
+
+
+ def write_data(self, stream, data):
+ 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'])
+ if data['filter'] == None: filter = "."
+ elif data['filter'] == []:
+ if self._version == 33: filter = "0"
+ else: filter = "PASS"
+ else: filter = ';'.join(data['filter'])
+ if data['qual'] == -1: qual = "."
+ else: qual = str(data['qual'])
+
+ output = [data['chrom'],
+ str(data['pos']+1), # change to 1-based position
+ data['id'],
+ data['ref'],
+ alt,
+ qual,
+ filter,
+ self.format_formatdata( data['info'], self._info, separator=";" ),
+ self.format_formatdata( data['format'], self._format, value=False ) ]
+
+ for s in self._samples:
+ output.append( self.format_formatdata( data[s], self._format, key=False ) )
+
+ stream.write( "\t".join(output) + "\n" )
+
+ def _parse_header(self, stream):
+ self._lineno = 0
+ for line in stream:
+ self._lineno += 1
+ if line.startswith('##'):
+ self.parse_header( line.strip() )
+ elif line.startswith('#'):
+ self.parse_heading( line.strip() )
+ self.enter_default_format()
+ else:
+ break
+ return line
+
+ def _parse(self, line, stream):
+ if len(line.strip()) > 0:
+ d = self.parse_data( line.strip() )
+ #if d: yield d
+ for line in stream:
+ self._lineno += 1
+ if self._lines and self._lineno > self._lines: raise StopIteration
+ d = self.parse_data( line.strip() )
+ #if d: yield d
+
+ ######################################################################################################
+ #
+ # API follows
+ #
+ ######################################################################################################
+
+ def getsamples(self):
+ """ List of samples in VCF file """
+ return self._samples
+
+ def setsamples(self,samples):
+ """ List of samples in VCF file """
+ self._samples = samples
+
+ def getheader(self):
+ """ List of header key-value pairs (strings) """
+ return self._header
+
+ def setheader(self,header):
+ """ List of header key-value pairs (strings) """
+ self._header = header
+
+ def getinfo(self):
+ """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+ return self._info
+
+ def setinfo(self,info):
+ """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+ self._info = info
+
+ def getformat(self):
+ """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+ return self._format
+
+ def setformat(self,format):
+ """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+ self._format = format
+
+ def getfilter(self):
+ """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+ return self._filter
+
+ def setfilter(self,filter):
+ """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+ 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
+
+ def setregions(self, regions):
+ 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
+
+ def ignoreerror(self, errorstring):
+ try: self._ignored_errors.add(self.__dict__[errorstring])
+ 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)
+
+ def parse(self, stream):
+ """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
+ last_line = self._parse_header(stream)
+ # 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)
+
+ def write(self, stream, datagenerator):
+ """ Writes a VCF file to a stream, using a data generator (or list) """
+ self.write_header(stream)
+ self.write_heading(stream)
+ for data in datagenerator: self.write_data(stream,data)
+
+ def writeheader(self, stream):
+ """ Writes a VCF header """
+ self.write_header(stream)
+ 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
+ # 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
+ while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
+ ref1 = ref1[:-1]
+ alt1 = alt1[:-1]
+ while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
+ ref2 = ref2[:-1]
+ alt2 = alt2[:-1]
+ # now, the alternative alleles must be identical
+ return alt1 == alt2
+
+###########################################################################################################
+###########################################################################################################
+## API functions added by Andreas
+###########################################################################################################
+
+ def connect( self, filename ):
+ '''connect to tabix file.'''
+ self.tabixfile = pysam.Tabixfile( filename )
+ self._parse_header(self.tabixfile.header)
+
+ def fetch(self,
+ reference = None,
+ start = None,
+ end = None,
+ region = None ):
+ """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
+
+ return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) )
+
+ def validate( self, record ):
+ '''validate vcf record.
+
+ returns a validated record.
+ '''
+
+ raise NotImplementedError( "needs to be checked" )
+
+ chrom, pos = record.chrom, record.pos
+
+ # check reference
+ ref = record.ref
+ if ref == ".":
+ self.error(str(record),self.MISSING_REF)
+ if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+ else: ref = ""
+ else:
+ for c in ref:
+ if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF)
+ if "N" in ref: ref = get_sequence(chrom,
+ pos,
+ pos+len(ref),
+ self._reference)
+
+ # make sure reference is sane
+ if self._reference:
+ left = max(0,self.pos-100)
+ faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference)
+ faref = faref_leftflank[pos-left:]
+ if faref != ref: self.error(str(record),self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
+ ref = faref
+
+ # check: format fields are defined
+ for f in record.format:
+ if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f)
+
+ # check: all filters are defined
+ for f in record.filter:
+ if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f)
+
+ # convert v3.3 alleles
+ if self._version == 33:
+ if len(ref) != 1: self.error(str(record),self.V33_BAD_REF)
+ newalts = []
+ have_deletions = False
+ 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<seq> and D<num>
+ 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)
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ 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)
+ if not s.endswith(addns) and addns != 'N'*len(addns):
+ self.error(str(record),self.V33_UNMATCHED_DELETION,
+ "(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
+ a = ref[len(s):] # new deletion, deleting from pos
+ else:
+ self.error(str(record),self.V33_BAD_ALLELE)
+ newalts.append(a)
+ alt = newalts
+ # 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)
+ ref += addn
+ 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]
+ pos -= 1
+ else:
+ # format v4.0 -- just check for nucleotides
+ for allele in alt:
+ if not alleleRegEx.match(allele):
+ self.error(str(record),self.V40_BAD_ALLELE,allele)
+
+
+ # check for leading nucleotide in indel calls
+ for allele in alt:
+ if len(allele) != len(ref):
+ if len(allele) == 0: self.error(str(record),self.ZERO_LENGTH_ALLELE)
+ if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
+ self.error(str(record),self.MISSING_INDEL_ALLELE_REF_BASE)
+
+ # trim trailing bases in alleles
+ 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]
+
+ # left-align alleles, if a reference is available
+ if self._leftalign and self._reference:
+ while left < pos:
+ movable = True
+ for allele in alt:
+ if len(allele) > len(ref):
+ longest, shortest = allele, ref
+ else:
+ longest, shortest = ref, allele
+ 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:
+ 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
+ alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+ pos -= 1
+
+__all__ = [
+ "VCF", "VCFRecord", ]
+
+
#include "pysam_util.h"
#include "errmod.h" // for pysam_dump
+#ifndef inline
+#define inline __inline
+#endif
+
// Definition of pysamerr
#include "stdio.h"
FILE * pysamerr = NULL;
void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
{
+ int x = 0;
fprintf(stderr,
"glf: ref_base=%i, max_mapQ=%i, min_lk=%i, depth=%i",
g->ref_base,
g->min_lk,
g->depth );
- int x = 0;
for (x = 0; x < 10; ++x)
fprintf(stderr, ", lk%x=%i, ", x, g->lk[x]);
int pysam_dispatch(int argc, char *argv[] )
{
-
+ extern int optind;
#ifdef _WIN32
setmode(fileno(stdout), O_BINARY);
setmode(fileno(stdin), O_BINARY);
knet_win32_init();
#endif
#endif
-
- extern int optind;
// reset getop
optind = 1;
uint8_t * pos )
{
int d = nbytes_new-nbytes_old;
+ int new_size;
+ size_t offset;
// no change
if (d == 0) return b;
- int new_size = d + b->data_len;
- size_t offset = pos - b->data;
+ new_size = d + b->data_len;
+ offset = pos - b->data;
//printf("d=%i, old=%i, new=%i, old_size=%i, new_size=%i\n",
// d, nbytes_old, nbytes_new, b->data_len, new_size);
# pysam versioning information
-__version__ = "0.4.1"
+__version__ = "0.5"
-__samtools_version__ = "0.1.12a"
+__samtools_version__ = "0.1.16"
-__tabix_version__ = "0.2.3"
+__tabix_version__ = "0.2.5"
#include "kstring.h"
#include "sam_header.h"
-int bam_is_be = 0;
+int bam_is_be = 0, bam_verbose = 2;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
/**************************
// with ESPIPE. Suppress the error message in this case.
if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
}
- else if (i == 0) fprintf(pysamerr, "[bam_header_read] EOF marker is absent.\n");
+ else if (i == 0) fprintf(pysamerr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
// read "BAM1"
magic_len = bam_read(fp, buf, 4);
if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+ else if (type == 'B') {
+ int32_t n, Bsize = bam_aux_type2size(*s);
+ memcpy(&n, s + 1, 4);
+ if (1 == Bsize) {
+ } else if (2 == Bsize) {
+ for (i = 0; i < n; i += 2)
+ bam_swap_endian_2p(s + 5 + i);
+ } else if (4 == Bsize) {
+ for (i = 0; i < n; i += 4)
+ bam_swap_endian_4p(s + 5 + i);
+ }
+ bam_swap_endian_4p(s+1);
+ }
}
}
else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
+ else if (type == 'B') {
+ uint8_t sub_type = *(s++);
+ int32_t n;
+ memcpy(&n, s, 4);
+ s += 4; // no point to the start of the array
+ kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
+ for (i = 0; i < n; ++i) {
+ kputc(',', &str);
+ if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
+ else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
+ else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
+ else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
+ else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
+ else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
+ else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
+ }
+ }
}
return str.s;
}
BAM library provides I/O and various operations on manipulating files
in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
- format. It now supports importing from or exporting to TAM, sorting,
+ format. It now supports importing from or exporting to SAM, sorting,
merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
@copyright Genome Research Ltd.
*/
+#define BAM_VERSION "0.1.16 (r963:234)"
+
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
*/
extern int bam_is_be;
+/*!
+ @abstract Verbose level between 0 and 3; 0 is supposed to disable all
+ debugging information, though this may not have been implemented.
+ */
+extern int bam_verbose;
+
/*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
extern unsigned char bam_nt16_table[256];
return b;
}
+static inline int bam_aux_type2size(int x)
+{
+ if (x == 'C' || x == 'c' || x == 'A') return 1;
+ else if (x == 'S' || x == 's') return 2;
+ else if (x == 'I' || x == 'i' || x == 'f') return 4;
+ else return 0;
+}
+
+
#endif
#define CALL_ETA 0.03f
#define CALL_MAX 256
#define CALL_DEFTHETA 0.83f
+#define DEF_MAPQ 20
#define CAP_DIST 25
bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
bca->min_baseQ = min_baseQ;
bca->e = errmod_init(1. - theta);
+ bca->min_frac = 0.002;
+ bca->min_support = 1;
return bca;
}
seqQ = is_indel? (p->aux>>8&0xff) : 99;
if (q < bca->min_baseQ) continue;
if (q > seqQ) q = seqQ;
- mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
+ mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+ mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
if (q > mapQ) q = mapQ;
if (q > 63) q = 63;
if (q < 4) q = 4;
}
bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
// collect annotations
- r->qsum[b] += q;
+ if (b < 4) r->qsum[b] += q;
++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
min_dist = p->b->core.l_qseq - 1 - p->qpos;
if (min_dist > p->qpos) min_dist = p->qpos;
x = call->n_alleles * (call->n_alleles + 1) / 2;
// get the possible genotypes
for (i = z = 0; i < call->n_alleles; ++i)
- for (j = i; j < call->n_alleles; ++j)
- g[z++] = call->a[i] * 5 + call->a[j];
+ for (j = 0; j <= i; ++j)
+ g[z++] = call->a[j] * 5 + call->a[i];
for (i = 0; i < n; ++i) {
uint8_t *PL = call->PL + x * i;
const bcf_callret1_t *r = calls + i;
typedef struct __bcf_callaux_t {
int capQ, min_baseQ;
- int openQ, extQ, tandemQ;
+ int openQ, extQ, tandemQ; // for indels
+ int min_support; // for collecting indel candidates
+ double min_frac; // for collecting indel candidates
// for internal uses
int max_bases;
int indel_types[4];
#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50
-#define MIN_SUPPORT_COEF 500
void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
{
extern void ks_introsort_uint32_t(int, uint32_t*);
int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
int N, K, l_run, ref_type, n_alt;
- char *inscns = 0, *ref2, *query;
+ char *inscns = 0, *ref2, *query, **ref_sample;
khash_t(rg) *hash = (khash_t(rg)*)rghash;
if (ref == 0 || bca == 0) return -1;
// mark filtered reads
// squeeze out identical types
for (i = 1, n_types = 1; i < m; ++i)
if (aux[i] != aux[i-1]) ++n_types;
- if (n_types == 1 || n_alt * MIN_SUPPORT_COEF < n_tot) { // no indels or too few supporting reads
+ if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
free(aux); return -1;
}
types = (int*)calloc(n_types, sizeof(int));
if (ref[i] == 0) break;
right = i;
}
+ /* The following block fixes a long-existing flaw in the INDEL
+ * calling model: the interference of nearby SNPs. However, it also
+ * reduces the power because sometimes, substitutions caused by
+ * indels are not distinguishable from true mutations. Multiple
+ * sequence realignment helps to increase the power.
+ */
+ { // construct per-sample consensus
+ int L = right - left + 1, max_i, max2_i;
+ uint32_t *cns, max, max2;
+ char *ref0, *r;
+ ref_sample = calloc(n, sizeof(void*));
+ cns = calloc(L, 4);
+ ref0 = calloc(L, 1);
+ for (i = 0; i < right - left; ++i)
+ ref0[i] = bam_nt16_table[(int)ref[i+left]];
+ for (s = 0; s < n; ++s) {
+ r = ref_sample[s] = calloc(L, 1);
+ memset(cns, 0, sizeof(int) * L);
+ // collect ref and non-ref counts
+ for (i = 0; i < n_plp[s]; ++i) {
+ bam_pileup1_t *p = plp[s] + i;
+ bam1_t *b = p->b;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *seq = bam1_seq(b);
+ int x = b->core.pos, y = 0;
+ for (k = 0; k < b->core.n_cigar; ++k) {
+ int op = cigar[k]&0xf;
+ int j, l = cigar[k]>>4;
+ if (op == BAM_CMATCH) {
+ for (j = 0; j < l; ++j)
+ if (x + j >= left && x + j < right)
+ cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;
+ x += l; y += l;
+ } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
+ else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ }
+ }
+ // determine the consensus
+ for (i = 0; i < right - left; ++i) r[i] = ref0[i];
+ max = max2 = 0; max_i = max2_i = -1;
+ for (i = 0; i < right - left; ++i) {
+ if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+ else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
+ }
+ if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
+ if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
+ if (max_i >= 0) r[max_i] = 15;
+ if (max2_i >= 0) r[max2_i] = 15;
+// for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], pysamerr); fputc('\n', pysamerr);
+ }
+ free(ref0); free(cns);
+ }
{ // the length of the homopolymer run around the current position
int c = bam_nt16_table[(int)ref[pos + 1]];
if (c == 15) l_run = 1;
else ir = est_indelreg(pos, ref, -types[t], 0);
if (ir > bca->indelreg) bca->indelreg = ir;
// fprintf(pysamerr, "%d, %d, %d\n", pos, types[t], ir);
- // write ref2
- for (k = 0, j = left; j <= pos; ++j)
- ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
- if (types[t] <= 0) j += -types[t];
- else for (l = 0; l < types[t]; ++l)
- ref2[k++] = inscns[t*max_ins + l];
- if (types[0] < 0) { // mask deleted sequences to avoid a particular error in the model.
- int jj, tmp = types[t] >= 0? -types[0] : -types[0] + types[t];
- for (jj = 0; jj < tmp && j < right && ref[j]; ++jj, ++j)
- ref2[k++] = 4;
- }
- for (; j < right && ref[j]; ++j)
- ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
- for (; k < max_ref2; ++k) ref2[k] = 4;
- if (j < right) right = j;
- // align each read to ref2
+ // realignment
for (s = K = 0; s < n; ++s) {
+ // write ref2
+ for (k = 0, j = left; j <= pos; ++j)
+ ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
+ if (types[t] <= 0) j += -types[t];
+ else for (l = 0; l < types[t]; ++l)
+ ref2[k++] = inscns[t*max_ins + l];
+ for (; j < right && ref[j]; ++j)
+ ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
+ for (; k < max_ref2; ++k) ref2[k] = 4;
+ if (j < right) right = j;
+ // align each read to ref2
for (i = 0; i < n_plp[s]; ++i, ++K) {
bam_pileup1_t *p = plp[s] + i;
- int qbeg, qend, tbeg, tend, sc;
+ int qbeg, qend, tbeg, tend, sc, kk;
uint8_t *seq = bam1_seq(p->b);
+ uint32_t *cigar = bam1_cigar(p->b);
+ if (p->b->core.flag&4) continue; // unmapped reads
+ // FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway.
+ for (kk = 0; kk < p->b->core.n_cigar; ++kk)
+ if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break;
+ if (kk < p->b->core.n_cigar) continue;
// FIXME: the following skips soft clips, but using them may be more sensitive.
// determine the start and end of sequences for alignment
qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499);
// pick the smaller between indelQ1 and indelQ2
indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
- p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ;
+ if (indelQ > 255) indelQ = 255;
+ if (seqQ > 255) seqQ = 255;
+ p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
-// fprintf(pysamerr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ);
+// fprintf(pysamerr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
}
}
// determine bca->indel_types[] and bca->inscns
}
free(score1); free(score2);
// free
+ for (i = 0; i < n; ++i) free(ref_sample[i]);
+ free(ref_sample);
free(types); free(inscns);
return n_alt > 0? 0 : -1;
}
--- /dev/null
+#include "pysam.h"
+
+/* This program demonstrates how to generate pileup from multiple BAMs
+ * simutaneously, to achieve random access and to use the BED interface.
+ * To compile this program separately, you may:
+ *
+ * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -L. -lbam -lz
+ */
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include "bam.h"
+
+typedef struct { // auxiliary data structure
+ bamFile fp; // the file handler
+ bam_iter_t iter; // NULL if a region not specified
+ int min_mapQ; // mapQ filter
+} aux_t;
+
+void *bed_read(const char *fn); // read a BED or position list file
+void bed_destroy(void *_h); // destroy the BED data structure
+int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps
+
+// This function reads a BAM alignment from one BAM file.
+static int read_bam(void *data, bam1_t *b) // read level filters better go here to avoid pileup
+{
+ aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
+ int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
+ if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+ return ret;
+}
+
+#ifdef _MAIN_BAM2DEPTH
+int main(int argc, char *argv[])
+#else
+int main_depth(int argc, char *argv[])
+#endif
+{
+ int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0;
+ const bam_pileup1_t **plp;
+ char *reg = 0; // specified region
+ void *bed = 0; // BED data structure
+ bam_header_t *h = 0; // BAM header of the 1st input
+ aux_t **data;
+ bam_mplp_t mplp;
+
+ // parse the command line
+ while ((n = getopt(argc, argv, "r:b:q:Q:")) >= 0) {
+ switch (n) {
+ case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header
+ case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
+ case 'q': baseQ = atoi(optarg); break; // base quality threshold
+ case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold
+ }
+ }
+ if (optind == argc) {
+ fprintf(pysamerr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-b in.bed] <in1.bam> [...]\n");
+ return 1;
+ }
+
+ // initialize the auxiliary data structures
+ n = argc - optind; // the number of BAMs on the command line
+ data = calloc(n, sizeof(void*)); // data[i] for the i-th input
+ beg = 0; end = 1<<30; tid = -1; // set the default region
+ for (i = 0; i < n; ++i) {
+ bam_header_t *htmp;
+ data[i] = calloc(1, sizeof(aux_t));
+ data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
+ data[i]->min_mapQ = mapQ; // set the mapQ filter
+ htmp = bam_header_read(data[i]->fp); // read the BAM header
+ if (i == 0) {
+ h = htmp; // keep the header of the 1st BAM
+ if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
+ } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
+ if (tid >= 0) { // if a region is specified and parsed successfully
+ bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index
+ data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
+ bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
+ }
+ }
+
+ // the core multi-pileup loop
+ mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
+ n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
+ plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp)
+ while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
+ if (pos < beg || pos >= end) continue; // out of range; skip
+ if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
+ fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
+ for (i = 0; i < n; ++i) { // base level filters have to go here
+ int j, m = 0;
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
+ if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
+ else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
+ }
+ printf("\t%d", n_plp[i] - m); // this the depth to output
+ }
+ putchar('\n');
+ }
+ free(n_plp); free(plp);
+ bam_mplp_destroy(mplp);
+
+ bam_header_destroy(h);
+ for (i = 0; i < n; ++i) {
+ bam_close(data[i]->fp);
+ if (data[i]->iter) bam_iter_destroy(data[i]->iter);
+ free(data[i]);
+ }
+ free(data); free(reg);
+ if (bed) bed_destroy(bed);
+ return 0;
+}
}
#define __skip_tag(s) do { \
- int type = toupper(*(s)); \
- ++(s); \
- if (type == 'C' || type == 'A') ++(s); \
- else if (type == 'S') (s) += 2; \
- else if (type == 'I' || type == 'F') (s) += 4; \
- else if (type == 'D') (s) += 8; \
- else if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
- } while (0)
+ int type = toupper(*(s)); \
+ ++(s); \
+ if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
+ else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
+ else (s) += bam_aux_type2size(type); \
+ } while(0)
uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
{
if (type == 'Z' || type == 'H') return (char*)s;
else return 0;
}
+
+#ifdef _WIN32
+double drand48()
+{
+ return (double)rand() / RAND_MAX;
+}
+#endif
--- /dev/null
+#include "pysam.h"
+
+/*\r
+\r
+bam_cat -- efficiently concatenates bam files\r
+\r
+bam_cat can be used to concatenate BAM files. Under special\r
+circumstances, it can be used as an alternative to 'samtools merge' to\r
+concatenate multiple sorted files into a single sorted file. For this\r
+to work each file must be sorted, and the sorted files must be given\r
+as command line arguments in order such that the final read in file i\r
+is less than or equal to the first read in file i+1.\r
+\r
+This code is derived from the bam_reheader function in samtools 0.1.8\r
+and modified to perform concatenation by Chris Saunders on behalf of\r
+Illumina.\r
+\r
+\r
+########## License:\r
+\r
+The MIT License\r
+\r
+Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd.\r
+Modified SAMtools work copyright (c) 2010 Illumina, Inc.\r
+\r
+Permission is hereby granted, free of charge, to any person obtaining a copy\r
+of this software and associated documentation files (the "Software"), to deal\r
+in the Software without restriction, including without limitation the rights\r
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\r
+copies of the Software, and to permit persons to whom the Software is\r
+furnished to do so, subject to the following conditions:\r
+\r
+The above copyright notice and this permission notice shall be included in\r
+all copies or substantial portions of the Software.\r
+\r
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\r
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\r
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\r
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\r
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\r
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\r
+THE SOFTWARE.\r
+\r
+*/\r
+\r
+\r
+/*\r
+makefile:\r
+"""\r
+CC=gcc\r
+CFLAGS+=-g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I$(SAMTOOLS_DIR)\r
+LDFLAGS+=-L$(SAMTOOLS_DIR)\r
+LDLIBS+=-lbam -lz\r
+\r
+all:bam_cat\r
+"""\r
+*/\r
+\r
+\r
+#include <stdio.h>\r
+#include <stdlib.h>\r
+#include <unistd.h>\r
+\r
+#include "bgzf.h"\r
+#include "bam.h"\r
+\r
+#define BUF_SIZE 0x10000\r
+\r
+#define GZIPID1 31\r
+#define GZIPID2 139\r
+\r
+#define BGZF_EMPTY_BLOCK_SIZE 28\r
+\r
+\r
+int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam)\r
+{\r
+ BGZF *fp;\r
+ FILE* fp_file;\r
+ uint8_t *buf;\r
+ uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE];\r
+ const int es=BGZF_EMPTY_BLOCK_SIZE;\r
+ int i;\r
+ \r
+ fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(stdout), "w");\r
+ if (fp == 0) {\r
+ fprintf(pysamerr, "[%s] ERROR: fail to open output file '%s'.\n", __func__, outbam);\r
+ return 1;\r
+ }\r
+ if (h) bam_header_write(fp, h);\r
+ \r
+ buf = (uint8_t*) malloc(BUF_SIZE);\r
+ for(i = 0; i < nfn; ++i){\r
+ BGZF *in;\r
+ bam_header_t *old;\r
+ int len,j;\r
+ \r
+ in = strcmp(fn[i], "-")? bam_open(fn[i], "r") : bam_dopen(fileno(stdin), "r");\r
+ if (in == 0) {\r
+ fprintf(pysamerr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]);\r
+ return -1;\r
+ }\r
+ if (in->open_mode != 'r') return -1;\r
+ \r
+ old = bam_header_read(in);\r
+ if (h == 0 && i == 0) bam_header_write(fp, old);\r
+ \r
+ if (in->block_offset < in->block_length) {\r
+ bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);\r
+ bgzf_flush(fp);\r
+ }\r
+ \r
+ j=0;\r
+#ifdef _USE_KNETFILE\r
+ fp_file=fp->x.fpw;\r
+ while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0) {\r
+#else \r
+ fp_file=fp->file;\r
+ while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) {\r
+#endif\r
+ if(len<es){\r
+ int diff=es-len;\r
+ if(j==0) {\r
+ fprintf(pysamerr, "[%s] ERROR: truncated file?: '%s'.\n", __func__, fn[i]);\r
+ return -1;\r
+ }\r
+ fwrite(ebuf, 1, len, fp_file);\r
+ memcpy(ebuf,ebuf+len,diff);\r
+ memcpy(ebuf+diff,buf,len);\r
+ } else {\r
+ if(j!=0) fwrite(ebuf, 1, es, fp_file);\r
+ len-= es;\r
+ memcpy(ebuf,buf+len,es);\r
+ fwrite(buf, 1, len, fp_file);\r
+ }\r
+ j=1;\r
+ }\r
+\r
+ /* check final gzip block */\r
+ {\r
+ const uint8_t gzip1=ebuf[0];\r
+ const uint8_t gzip2=ebuf[1];\r
+ const uint32_t isize=*((uint32_t*)(ebuf+es-4));\r
+ if(((gzip1!=GZIPID1) || (gzip2!=GZIPID2)) || (isize!=0)) {\r
+ fprintf(pysamerr, "[%s] WARNING: Unexpected block structure in file '%s'.", __func__, fn[i]);\r
+ fprintf(pysamerr, " Possible output corruption.\n");\r
+ fwrite(ebuf, 1, es, fp_file);\r
+ }\r
+ }\r
+ bam_header_destroy(old);\r
+ bgzf_close(in);\r
+ }\r
+ free(buf);\r
+ bgzf_close(fp);\r
+ return 0;\r
+}\r
+\r
+\r
+\r
+int main_cat(int argc, char *argv[])\r
+{\r
+ bam_header_t *h = 0;\r
+ char *outfn = 0;\r
+ int c, ret;\r
+ while ((c = getopt(argc, argv, "h:o:")) >= 0) {\r
+ switch (c) {\r
+ case 'h': {\r
+ tamFile fph = sam_open(optarg);\r
+ if (fph == 0) {\r
+ fprintf(pysamerr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, argv[1]);\r
+ return 1;\r
+ }\r
+ h = sam_header_read(fph);\r
+ sam_close(fph);\r
+ break;\r
+ }\r
+ case 'o': outfn = strdup(optarg); break;\r
+ }\r
+ }\r
+ if (argc - optind < 2) {\r
+ fprintf(pysamerr, "Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [...]\n");\r
+ return 1;\r
+ }\r
+ ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-");\r
+ free(outfn);\r
+ return ret;\r
+}\r
memcpy(s, str->s + 5, str->l - 5);
s[str->l - 5] = 0;
doff += size;
+ } else if (type == 'B') {
+ int32_t n = 0, Bsize, k = 0, size;
+ char *p;
+ if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
+ Bsize = bam_aux_type2size(str->s[5]); // the size of each element
+ for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
+ if (*p == ',') ++n;
+ p = str->s + 7; // now p points to the first number in the array
+ size = 6 + Bsize * n; // total number of bytes allocated to this tag
+ s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
+ *s++ = 'B'; *s++ = str->s[5];
+ memcpy(s, &n, 4); s += 4; // write the number of elements
+ if (str->s[5] == 'c') while (p < str->s + str->l) ((int8_t*)s)[k++] = (int8_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++] = (uint8_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++] = (int16_t)strtol(p, &p, 0), ++p; // FIXME: avoid unaligned memory
+ else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++] = (int32_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
+ else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtof(p, &p), ++p;
+ else parse_error(fp->n_lines, "unrecognized array type");
+ s += Bsize * n; doff += size;
} else parse_error(fp->n_lines, "unrecognized type");
if (dret == '\n' || dret == '\r') break;
}
}
merge_chunks(idx);
fill_missing(idx);
- if (ret >= 0)
- while ((ret = bam_read1(fp, b)) >= 0) ++n_no_coor;
+ if (ret >= 0) {
+ while ((ret = bam_read1(fp, b)) >= 0) {
+ ++n_no_coor;
+ if (c->tid >= 0 && n_no_coor) {
+ fprintf(pysamerr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+ exit(1);
+ }
+ }
+ }
if (ret < -1) fprintf(pysamerr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
free(b->data); free(b);
idx->n_no_coor = n_no_coor;
uint32_t c[4];
} glf_call_aux_t;
-char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
-
/*
P(<b1,b2>) = \theta \sum_{i=1}^{N-1} 1/i
P(D|<b1,b2>) = \sum_{k=1}^{N-1} p_k 1/2 [(k/N)^n_2(1-k/N)^n_1 + (k/N)^n1(1-k/N)^n_2]
#include "kaln.h"
#include "kprobaln.h"
+char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+
void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
{
uint8_t *seq = bam1_seq(b);
return (int)(t + .499);
}
-int bam_prob_realn_core(bam1_t *b, const char *ref, int apply_baq)
+int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
{
- int k, i, bw, x, y, yb, ye, xb, xe;
+ int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1;
uint32_t *cigar = bam1_cigar(b);
bam1_core_t *c = &b->core;
kpa_par_t conf = kpa_par_def;
uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b);
- if (c->flag & BAM_FUNMAP) return -1; // do nothing
+ if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0) return -1; // do nothing
// test if BQ or ZQ is present
if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
s = calloc(c->l_qseq, 1);
for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
r = calloc(xe - xb, 1);
- for (i = xb; i < xe; ++i)
+ for (i = xb; i < xe; ++i) {
+ if (ref[i] == 0) { xe = i; break; }
r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
+ }
state = calloc(c->l_qseq, sizeof(int));
q = calloc(c->l_qseq, 1);
kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
- for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
- int op = cigar[k]&0xf, l = cigar[k]>>4;
- if (op == BAM_CMATCH) {
- for (i = y; i < y + l; ++i) {
- if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
- else bq[i] = bq[i] < q[i]? bq[i] : q[i];
- }
- x += l; y += l;
- } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
- else if (op == BAM_CDEL) x += l;
+ if (!extend_baq) { // in this block, bq[] is capped by base quality qual[]
+ for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k]&0xf, l = cigar[k]>>4;
+ if (op == BAM_CMATCH) {
+ for (i = y; i < y + l; ++i) {
+ if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
+ else bq[i] = bq[i] < q[i]? bq[i] : q[i];
+ }
+ x += l; y += l;
+ } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+ else if (op == BAM_CDEL) x += l;
+ }
+ for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
+ } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!)
+ uint8_t *left, *rght;
+ left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
+ for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
+ int op = cigar[k]&0xf, l = cigar[k]>>4;
+ if (op == BAM_CMATCH) {
+ for (i = y; i < y + l; ++i)
+ bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i];
+ for (left[y] = bq[y], i = y + 1; i < y + l; ++i)
+ left[i] = bq[i] > left[i-1]? bq[i] : left[i-1];
+ for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i)
+ rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1];
+ for (i = y; i < y + l; ++i)
+ bq[i] = left[i] < rght[i]? left[i] : rght[i];
+ x += l; y += l;
+ } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
+ else if (op == BAM_CDEL) x += l;
+ }
+ for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ
+ free(left); free(rght);
}
- for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
if (apply_baq) {
for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual
bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq);
int bam_fillmd(int argc, char *argv[])
{
- int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, apply_baq;
+ int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag;
samfile_t *fp, *fpout = 0;
faidx_t *fai;
char *ref = 0, mode_w[8], mode_r[8];
bam1_t *b;
- is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = apply_baq = capQ = 0;
+ is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0;
mode_w[0] = mode_r[0] = 0;
strcpy(mode_r, "r"); strcpy(mode_w, "w");
- while ((c = getopt(argc, argv, "reubSC:n:A")) >= 0) {
+ while ((c = getopt(argc, argv, "EreubSC:n:A")) >= 0) {
switch (c) {
case 'r': is_realn = 1; break;
case 'e': is_equal = 1; break;
case 'S': is_sam_in = 1; break;
case 'n': max_nm = atoi(optarg); break;
case 'C': capQ = atoi(optarg); break;
- case 'A': apply_baq = 1; break;
+ case 'A': baq_flag |= 1; break;
+ case 'E': baq_flag |= 2; break;
default: fprintf(pysamerr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
}
}
fprintf(pysamerr, " -b compressed BAM output\n");
fprintf(pysamerr, " -S the input is SAM with header\n");
fprintf(pysamerr, " -A modify the quality string\n");
- fprintf(pysamerr, " -r read-independent local realignment\n\n");
+ fprintf(pysamerr, " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n");
+ fprintf(pysamerr, " -E extended BAQ for better sensitivity but lower specificity\n\n");
return 1;
}
fp = samopen(argv[optind], mode_r, 0);
fprintf(pysamerr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
fp->header->target_name[tid]);
}
- if (is_realn) bam_prob_realn_core(b, ref, apply_baq);
+ if (is_realn) bam_prob_realn_core(b, ref, baq_flag);
if (capQ > 10) {
int q = bam_cap_mapQ(b, ref, capQ);
if (b->core.qual > q) b->core.qual = q;
if (proposed_indels) // the first element gives the size of the array
r = bam_maqindel(m, pos, d->ido, pu, d->ref, proposed_indels[0], proposed_indels+1);
else r = bam_maqindel(m, pos, d->ido, pu, d->ref, 0, 0);
-
}
// when only variant sites are asked for, test if the site is a variant
if ((d->format & BAM_PLF_CNS) && (d->format & BAM_PLF_VAR_ONLY)) {
int c, is_SAM = 0;
char *fn_list = 0, *fn_fa = 0, *fn_pos = 0;
pu_data_t *d = (pu_data_t*)calloc(1, sizeof(pu_data_t));
- d->max_depth = 1024; d->tid = -1; d->mask = BAM_DEF_MASK; d->min_baseQ = 13;
+ d->max_depth = 1024; d->tid = -1; d->mask = BAM_DEF_MASK; d->min_baseQ = 13;
d->c = bam_maqcns_init();
d->c->errmod = BAM_ERRMOD_MAQ2; // change the default model
d->ido = bam_maqindel_opt_init();
fprintf(pysamerr, " -G FLOAT prior of an indel between two haplotypes (for -c) [%.4g]\n", d->ido->r_indel);
fprintf(pysamerr, " -I INT phred prob. of an indel in sequencing/prep. (for -c) [%d]\n", d->ido->q_indel);
fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Warning: Please use the `mpileup' command instead `pileup'. `Pileup' is deprecated!\n\n");
free(fn_list); free(fn_fa); free(d);
return 1;
}
#define MPLP_FMT_DP 0x100
#define MPLP_FMT_SP 0x200
#define MPLP_NO_INDEL 0x400
+#define MPLP_EXT_BAQ 0x800
+#define MPLP_ILLUMINA13 0x1000
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
typedef struct {
- int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth;
- int openQ, extQ, tandemQ;
- char *reg, *fn_pos, *pl_list;
+ int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth;
+ int openQ, extQ, tandemQ, min_support; // for indels
+ double min_frac; // for indels
+ char *reg, *pl_list;
faidx_t *fai;
- kh_64_t *hash;
+ void *bed, *rghash;
} mplp_conf_t;
typedef struct {
bamFile fp;
bam_iter_t iter;
- int min_mq, flag, ref_id, capQ_thres;
+ bam_header_t *h;
+ int ref_id;
char *ref;
+ const mplp_conf_t *conf;
} mplp_aux_t;
typedef struct {
int has_ref;
ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
if (ret < 0) break;
+ if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
+ skip = 1;
+ continue;
+ }
+ if (ma->conf->bed) { // test overlap
+ skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
+ if (skip) continue;
+ }
+ if (ma->conf->rghash) { // exclude read groups
+ uint8_t *rg = bam_aux_get(b, "RG");
+ skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
+ if (skip) continue;
+ }
+ if (ma->conf->flag & MPLP_ILLUMINA13) {
+ int i;
+ uint8_t *qual = bam1_qual(b);
+ for (i = 0; i < b->core.l_qseq; ++i)
+ qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+ }
has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
skip = 0;
- if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
- if (has_ref && ma->capQ_thres > 10) {
- int q = bam_cap_mapQ(b, ma->ref, ma->capQ_thres);
+ if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
+ if (has_ref && ma->conf->capQ_thres > 10) {
+ int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres);
if (q < 0) skip = 1;
else if (b->core.qual > q) b->core.qual = q;
- } else if (b->core.flag&BAM_FUNMAP) skip = 1;
- else if (b->core.qual < ma->min_mq) skip = 1;
- else if ((ma->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
+ }
+ else if (b->core.qual < ma->conf->min_mq) skip = 1;
+ else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
} while (skip);
return ret;
}
q = bam_aux_get(p->b, "RG");
if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
- assert(id >= 0 && id < m->n);
+ if (id < 0 || id >= m->n) {
+ assert(q); // otherwise a bug
+ fprintf(pysamerr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
+ exit(1);
+ }
if (m->n_plp[id] == m->m_plp[id]) {
m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
extern void bcf_call_del_rghash(void *rghash);
mplp_aux_t **data;
- int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth;
+ int i, tid, pos, *n_plp, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid, max_depth, max_indel_depth;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_header_t *h = 0;
char *ref;
- khash_t(64) *hash = 0;
void *rghash = 0;
bcf_callaux_t *bca = 0;
for (i = 0; i < n; ++i) {
bam_header_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
- data[i]->min_mq = conf->min_mq;
- data[i]->flag = conf->flag;
- data[i]->capQ_thres = conf->capQ_thres;
data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
+ data[i]->conf = conf;
h_tmp = bam_header_read(data[i]->fp);
+ data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
bam_smpl_add(sm, fn[i], h_tmp->text);
rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
if (conf->reg) {
gplp.plp = calloc(sm->n, sizeof(void*));
fprintf(pysamerr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
- if (conf->fn_pos) hash = load_pos(conf->fn_pos, h);
// write the VCF header
if (conf->flag & MPLP_GLF) {
kstring_t s;
bh->l_smpl = s.l;
bh->sname = malloc(s.l);
memcpy(bh->sname, s.s, s.l);
- bh->l_txt = 0;
+ bh->txt = malloc(strlen(BAM_VERSION) + 64);
+ bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
free(s.s);
bcf_hdr_sync(bh);
bcf_hdr_write(bp, bh);
bcr = calloc(sm->n, sizeof(bcf_callret1_t));
bca->rghash = rghash;
bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
+ bca->min_frac = conf->min_frac;
+ bca->min_support = conf->min_support;
}
ref_tid = -1; ref = 0;
iter = bam_mplp_init(n, mplp_func, (void**)data);
fprintf(pysamerr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
if (max_depth * sm->n < 8000) {
max_depth = 8000 / sm->n;
- fprintf(pysamerr, "<%s> Set max per-sample depth to %d\n", __func__, max_depth);
+ fprintf(pysamerr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
}
+ max_indel_depth = conf->max_indel_depth * sm->n;
bam_mplp_set_maxcnt(iter, max_depth);
while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
- if (hash) {
- khint_t k;
- k = kh_get(64, hash, (uint64_t)tid<<32 | pos);
- if (k == kh_end(hash)) continue;
- }
+ if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
if (tid != ref_tid) {
free(ref); ref = 0;
if (conf->fai) ref = fai_fetch(conf->fai, h->target_name[tid], &ref_len);
ref_tid = tid;
}
if (conf->flag & MPLP_GLF) {
- int _ref0, ref16;
+ int total_depth, _ref0, ref16;
bcf1_t *b = calloc(1, sizeof(bcf1_t));
+ for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp);
_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
ref16 = bam_nt16_table[_ref0];
bcf_write(bp, bh, b);
bcf_destroy(b);
// call indels
- if (!(conf->flag&MPLP_NO_INDEL) && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
+ if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
bcf_call_del_rghash(rghash);
- if (hash) { // free the hash table
- khint_t k;
- for (k = kh_begin(hash); k < kh_end(hash); ++k)
- if (kh_exist(hash, k)) free(kh_val(hash, k));
- kh_destroy(64, hash);
- }
bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
bam_mplp_destroy(iter);
bam_header_destroy(h);
}
#define MAX_PATH_LEN 1024
-int read_file_list(const char *file_list,int *n,char **argv[])
+static int read_file_list(const char *file_list,int *n,char **argv[])
{
char buf[MAX_PATH_LEN];
int len, nfiles;
int c;
const char *file_list = NULL;
char **fn = NULL;
- int nfiles = 0;
+ int nfiles = 0, use_orphan = 0;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.max_mq = 60;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
- mplp.max_depth = 250;
+ mplp.max_depth = 250; mplp.max_indel_depth = 250;
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
+ mplp.min_frac = 0.002; mplp.min_support = 1;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:BDSd:b:P:o:e:h:I")) >= 0) {
+ while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6")) >= 0) {
switch (c) {
case 'f':
mplp.fai = fai_load(optarg);
break;
case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg = strdup(optarg); break;
- case 'l': mplp.fn_pos = strdup(optarg); break;
+ case 'l': mplp.bed = bed_read(optarg); break;
case 'P': mplp.pl_list = strdup(optarg); break;
case 'g': mplp.flag |= MPLP_GLF; break;
case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
- case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;
- case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
+ case 'B': mplp.flag &= ~MPLP_REALN; break;
case 'R': mplp.flag |= MPLP_REALN; break;
case 'D': mplp.flag |= MPLP_FMT_DP; break;
case 'S': mplp.flag |= MPLP_FMT_SP; break;
case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+ case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
+ case '6': mplp.flag |= MPLP_ILLUMINA13; break;
case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'M': mplp.max_mq = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'o': mplp.openQ = atoi(optarg); break;
case 'e': mplp.extQ = atoi(optarg); break;
case 'h': mplp.tandemQ = atoi(optarg); break;
+ case 'A': use_orphan = 1; break;
+ case 'F': mplp.min_frac = atof(optarg); break;
+ case 'm': mplp.min_support = atoi(optarg); break;
+ case 'L': mplp.max_indel_depth = atoi(optarg); break;
+ case 'G': {
+ FILE *fp_rg;
+ char buf[1024];
+ mplp.rghash = bcf_str2id_init();
+ if ((fp_rg = fopen(optarg, "r")) == 0)
+ fprintf(pysamerr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
+ while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
+ bcf_str2id_add(mplp.rghash, strdup(buf));
+ fclose(fp_rg);
+ }
+ break;
}
}
+ if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
if (argc == 1) {
fprintf(pysamerr, "\n");
- fprintf(pysamerr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
- fprintf(pysamerr, "Options: -f FILE reference sequence file [null]\n");
- fprintf(pysamerr, " -r STR region in which pileup is generated [null]\n");
- fprintf(pysamerr, " -l FILE list of positions (format: chr pos) [null]\n");
- fprintf(pysamerr, " -b FILE list of input BAM files [null]\n");
- fprintf(pysamerr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
- fprintf(pysamerr, " -Q INT min base quality [%d]\n", mplp.min_baseQ);
- fprintf(pysamerr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
- fprintf(pysamerr, " -d INT max per-sample depth [%d]\n", mplp.max_depth);
- fprintf(pysamerr, " -P STR comma separated list of platforms for indels [all]\n");
- fprintf(pysamerr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
- fprintf(pysamerr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
- fprintf(pysamerr, " -h INT coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
- fprintf(pysamerr, " -g generate BCF output\n");
- fprintf(pysamerr, " -u do not compress BCF output\n");
- fprintf(pysamerr, " -B disable BAQ computation\n");
- fprintf(pysamerr, " -D output per-sample DP\n");
- fprintf(pysamerr, " -S output per-sample SP (strand bias P-value, slow)\n");
- fprintf(pysamerr, " -I do not perform indel calling\n");
+ fprintf(pysamerr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+ fprintf(pysamerr, "Input options:\n\n");
+ fprintf(pysamerr, " -6 assume the quality is in the Illumina-1.3+ encoding\n");
+ fprintf(pysamerr, " -A count anomalous read pairs\n");
+ fprintf(pysamerr, " -B disable BAQ computation\n");
+ fprintf(pysamerr, " -b FILE list of input BAM files [null]\n");
+ fprintf(pysamerr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
+ fprintf(pysamerr, " -E extended BAQ for higher sensitivity but lower specificity\n");
+ fprintf(pysamerr, " -f FILE faidx indexed reference sequence file [null]\n");
+ fprintf(pysamerr, " -G FILE exclude read groups listed in FILE [null]\n");
+ fprintf(pysamerr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
+ fprintf(pysamerr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
+ fprintf(pysamerr, " -r STR region in which pileup is generated [null]\n");
+ fprintf(pysamerr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
+ fprintf(pysamerr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+ fprintf(pysamerr, "\nOutput options:\n\n");
+ fprintf(pysamerr, " -D output per-sample DP in BCF (require -g/-u)\n");
+ fprintf(pysamerr, " -g generate BCF output (genotype likelihoods)\n");
+ fprintf(pysamerr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
+ fprintf(pysamerr, " -u generate uncompress BCF output\n");
+ fprintf(pysamerr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
+ fprintf(pysamerr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
+ fprintf(pysamerr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
+ fprintf(pysamerr, " -h INT coefficient for homopolymer errors [%d]\n", mplp.tandemQ);
+ fprintf(pysamerr, " -I do not perform indel calling\n");
+ fprintf(pysamerr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
+ fprintf(pysamerr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
+ fprintf(pysamerr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+ fprintf(pysamerr, " -P STR comma separated list of platforms for indels [all]\n");
fprintf(pysamerr, "\n");
fprintf(pysamerr, "Notes: Assuming diploid individuals.\n\n");
return 1;
}
- if ( file_list )
- {
+ if (file_list) {
if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
mpileup(&mplp,nfiles,fn);
for (c=0; c<nfiles; c++) free(fn[c]);
free(fn);
- }
- else
- mpileup(&mplp, argc - optind, argv + optind);
+ } else mpileup(&mplp, argc - optind, argv + optind);
+ if (mplp.rghash) bcf_str2id_thorough_destroy(mplp.rghash);
free(mplp.reg); free(mplp.pl_list);
if (mplp.fai) fai_destroy(mplp.fai);
+ if (mplp.bed) bed_destroy(mplp.bed);
return 0;
}
#define MERGE_RG 1
#define MERGE_UNCOMP 2
+#define MERGE_LEVEL1 4
+#define MERGE_FORCE 8
/*!
@abstract Merge multiple sorted BAM.
h->i = i;
h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
- h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)h->b->core.pos<<1 | bam1_strand(h->b);
+ h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
h->idx = idx++;
}
else h->pos = HEAP_EMPTY;
}
- if (flag & MERGE_UNCOMP) {
- fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
- } else {
- fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
- }
+ if (flag & MERGE_UNCOMP) fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
+ else if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(fileno(stdout), "w1");
+ else fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
if (fpout == 0) {
fprintf(pysamerr, "[%s] fail to create the output file.\n", __func__);
return -1;
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
bam1_t *b = heap->b;
- if ((flag & MERGE_RG) && bam_aux_get(b, "RG") == 0)
+ if (flag & MERGE_RG) {
+ uint8_t *rg = bam_aux_get(b, "RG");
+ if (rg) bam_aux_del(b, rg);
bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
+ }
bam_write1_core(fpout, &b->core, b->data_len, b->data);
if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
- heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)b->core.pos<<1 | bam1_strand(b);
+ heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
heap->idx = idx++;
} else if (j == -1) {
heap->pos = HEAP_EMPTY;
int c, is_by_qname = 0, flag = 0, ret = 0;
char *fn_headers = NULL, *reg = 0;
- while ((c = getopt(argc, argv, "h:nruR:")) >= 0) {
+ while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
switch (c) {
case 'r': flag |= MERGE_RG; break;
+ case 'f': flag |= MERGE_FORCE; break;
case 'h': fn_headers = strdup(optarg); break;
case 'n': is_by_qname = 1; break;
+ case '1': flag |= MERGE_LEVEL1; break;
case 'u': flag |= MERGE_UNCOMP; break;
case 'R': reg = strdup(optarg); break;
}
fprintf(pysamerr, "Options: -n sort by read names\n");
fprintf(pysamerr, " -r attach RG tag (inferred from file names)\n");
fprintf(pysamerr, " -u uncompressed BAM output\n");
+ fprintf(pysamerr, " -f overwrite the output BAM if exist\n");
+ fprintf(pysamerr, " -1 compress level 1\n");
fprintf(pysamerr, " -R STR merge file in the specified region STR [all]\n");
fprintf(pysamerr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
fprintf(pysamerr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
fprintf(pysamerr, " the header dictionary in merging.\n\n");
return 1;
}
+ if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
+ FILE *fp = fopen(argv[optind], "rb");
+ if (fp != NULL) {
+ fclose(fp);
+ fprintf(pysamerr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
+ return 1;
+ }
+ }
if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
free(reg);
free(fn_headers);
{
if (g_is_by_qname) {
int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
- return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos))));
- } else return (((uint64_t)a->core.tid<<32|a->core.pos) < ((uint64_t)b->core.tid<<32|b->core.pos));
+ return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
+ } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
}
KSORT_INIT(sort, bam1_p, bam1_lt)
static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
{
- char *name;
+ char *name, mode[3];
int i;
bamFile fp;
ks_mergesort(sort, k, buf, 0);
name = (char*)calloc(strlen(prefix) + 20, 1);
- if (n >= 0) sprintf(name, "%s.%.4d.bam", prefix, n);
- else sprintf(name, "%s.bam", prefix);
- fp = is_stdout? bam_dopen(fileno(stdout), "w") : bam_open(name, "w");
+ if (n >= 0) {
+ sprintf(name, "%s.%.4d.bam", prefix, n);
+ strcpy(mode, "w1");
+ } else {
+ sprintf(name, "%s.bam", prefix);
+ strcpy(mode, "w");
+ }
+ fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
if (fp == 0) {
fprintf(pysamerr, "[sort_blocks] fail to create file %s.\n", name);
free(name);
#include "bam.h"
typedef struct {
- long long n_reads, n_mapped, n_pair_all, n_pair_map, n_pair_good;
- long long n_sgltn, n_read1, n_read2;
- long long n_qcfail, n_dup;
- long long n_diffchr, n_diffhigh;
+ long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
+ long long n_sgltn[2], n_read1[2], n_read2[2];
+ long long n_dup[2];
+ long long n_diffchr[2], n_diffhigh[2];
} bam_flagstat_t;
#define flagstat_loop(s, c) do { \
- ++(s)->n_reads; \
+ int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0; \
+ ++(s)->n_reads[w]; \
if ((c)->flag & BAM_FPAIRED) { \
- ++(s)->n_pair_all; \
- if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good; \
- if ((c)->flag & BAM_FREAD1) ++(s)->n_read1; \
- if ((c)->flag & BAM_FREAD2) ++(s)->n_read2; \
- if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn; \
+ ++(s)->n_pair_all[w]; \
+ if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good[w]; \
+ if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w]; \
+ if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w]; \
+ if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w]; \
if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
- ++(s)->n_pair_map; \
+ ++(s)->n_pair_map[w]; \
if ((c)->mtid != (c)->tid) { \
- ++(s)->n_diffchr; \
- if ((c)->qual >= 5) ++(s)->n_diffhigh; \
+ ++(s)->n_diffchr[w]; \
+ if ((c)->qual >= 5) ++(s)->n_diffhigh[w]; \
} \
} \
} \
- if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped; \
- if ((c)->flag & BAM_FQCFAIL) ++(s)->n_qcfail; \
- if ((c)->flag & BAM_FDUP) ++(s)->n_dup; \
+ if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w]; \
+ if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w]; \
} while (0)
bam_flagstat_t *bam_flagstat_core(bamFile fp)
assert(fp);
header = bam_header_read(fp);
s = bam_flagstat_core(fp);
- printf("%lld in total\n", s->n_reads);
- printf("%lld QC failure\n", s->n_qcfail);
- printf("%lld duplicates\n", s->n_dup);
- printf("%lld mapped (%.2f%%)\n", s->n_mapped, (float)s->n_mapped / s->n_reads * 100.0);
- printf("%lld paired in sequencing\n", s->n_pair_all);
- printf("%lld read1\n", s->n_read1);
- printf("%lld read2\n", s->n_read2);
- printf("%lld properly paired (%.2f%%)\n", s->n_pair_good, (float)s->n_pair_good / s->n_pair_all * 100.0);
- printf("%lld with itself and mate mapped\n", s->n_pair_map);
- printf("%lld singletons (%.2f%%)\n", s->n_sgltn, (float)s->n_sgltn / s->n_pair_all * 100.0);
- printf("%lld with mate mapped to a different chr\n", s->n_diffchr);
- printf("%lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh);
+ printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
+ printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
+ printf("%lld + %lld mapped (%.2f%%:%.2f%%)\n", s->n_mapped[0], s->n_mapped[1], (float)s->n_mapped[0] / s->n_reads[0] * 100.0, (float)s->n_mapped[1] / s->n_reads[1] * 100.0);
+ printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
+ printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
+ printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
+ printf("%lld + %lld properly paired (%.2f%%:%.2f%%)\n", s->n_pair_good[0], s->n_pair_good[1], (float)s->n_pair_good[0] / s->n_pair_all[0] * 100.0, (float)s->n_pair_good[1] / s->n_pair_all[1] * 100.0);
+ printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
+ printf("%lld + %lld singletons (%.2f%%:%.2f%%)\n", s->n_sgltn[0], s->n_sgltn[1], (float)s->n_sgltn[0] / s->n_pair_all[0] * 100.0, (float)s->n_sgltn[1] / s->n_pair_all[1] * 100.0);
+ printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
+ printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
free(s);
bam_header_destroy(header);
bam_close(fp);
{
tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
tv->is_dot = 1;
- tv->idx = bam_index_load(fn);
- if (tv->idx == 0) exit(1);
tv->fp = bam_open(fn, "r");
bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
assert(tv->fp);
tv->header = bam_header_read(tv->fp);
+ tv->idx = bam_index_load(fn);
+ if (tv->idx == 0) exit(1);
tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
if (fn_fa) tv->fai = fai_load(fn_fa);
tv->bmc = bam_maqcns_init();
ks_tokaux_t aux;
// set ref, alt, flt, info, fmt
b->ref = b->alt = b->flt = b->info = b->fmt = 0;
- for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
- if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
+ for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
+ if (*p == 0 && p+1 != b->str + b->l_str) {
+ if (n == 5) {
+ ++n;
+ break;
+ } else tmp[n++] = p + 1;
+ }
+ }
if (n != 5) {
- fprintf(pysamerr, "[%s] incorrect number of fields (%d != 5). Corrupted file?\n", __func__, n);
+ fprintf(pysamerr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
return -1;
}
b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
} else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
b->gi[i].len = 2;
- } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
- || b->gi[i].fmt == bcf_str2int("SP", 2))
- {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
b->gi[i].len = 1;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ b->gi[i].len = 4;
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
}
}
} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
kputw(((uint16_t*)b->gi[i].data)[j], s);
- } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
kputw(((uint8_t*)b->gi[i].data)[j], s);
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ kputw(((int32_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
int y = ((uint8_t*)b->gi[i].data)[j];
if (y>>7&1) {
if (k > 0) kputc(',', s);
ksprintf(s, "%.2f", d[k]);
}
- }
+ } else kputc('.', s); // custom fields
}
}
}
int vcf_close(bcf_t *bp);
// read the VCF/BCF header
bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
+ // read the sequence dictionary from a separate file; required for VCF->BCF conversion
+ int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn);
// read a VCF/BCF record; return -1 on end-of-file and <-1 for errors
int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
// write the VCF header
int bcf_gl2pl(bcf1_t *b);
// if the site is an indel
int bcf_is_indel(const bcf1_t *b);
+ bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list);
+ int bcf_subsam(int n_smpl, int *list, bcf1_t *b);
+ // move GT to the first FORMAT field
+ int bcf_fix_gt(bcf1_t *b);
+ // update PL generated by old samtools
+ int bcf_fix_pl(bcf1_t *b);
// string hash table
void *bcf_build_refhash(bcf_hdr_t *h);
void bcf_str2id_destroy(void *_hash);
+ void bcf_str2id_thorough_destroy(void *_hash);
int bcf_str2id_add(void *_hash, const char *str);
int bcf_str2id(void *_hash, const char *str);
void *bcf_str2id_init();
for (k = j = 0; k < 4; ++k) {
for (l = k; l < 4; ++l) {
int t, x = map[k], y = map[l];
- if (x > y) t = x, x = y, y = t;
- g[j++] = p[x * b->n_alleles - x * (x-1) / 2 + (y - x)];
+ if (x > y) t = x, x = y, y = t; // swap
+ g[j++] = p[y * (y+1) / 2 + x];
}
}
printf("%s\t%d\t%c", h->ns[b->tid], b->pos+1, *b->ref);
#include "pysam.h"
+#include <string.h>
+#include <math.h>
#include "bcf.h"
#include "kstring.h"
#include "khash.h"
if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
}
+void bcf_str2id_thorough_destroy(void *_hash)
+{
+ khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
+ khint_t k;
+ if (hash == 0) return;
+ for (k = 0; k < kh_end(hash); ++k)
+ if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+ kh_destroy(str2id, hash);
+}
+
int bcf_str2id(void *_hash, const char *str)
{
khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
int bcf_shrink_alt(bcf1_t *b, int n)
{
char *p;
- int i, j, k, *z, n_smpl = b->n_smpl;
+ int i, j, k, n_smpl = b->n_smpl;
if (b->n_alleles <= n) return -1;
+ // update ALT
if (n > 1) {
for (p = b->alt, k = 1; *p; ++p)
if (*p == ',' && ++k == n) break;
++p;
memmove(p, b->flt, b->str + b->l_str - b->flt);
b->l_str -= b->flt - p;
- z = alloca(sizeof(int) / 2 * n * (n+1));
- for (i = k = 0; i < n; ++i)
- for (j = 0; j < n - i; ++j)
- z[k++] = i * b->n_alleles + j;
+ // update PL
for (i = 0; i < b->n_gi; ++i) {
bcf_ginfo_t *g = b->gi + i;
if (g->fmt == bcf_str2int("PL", 2)) {
g->len = n * (n + 1) / 2;
for (l = k = 0; l < n_smpl; ++l) {
uint8_t *dl = d + l * x;
- for (j = 0; j < g->len; ++j) d[k++] = dl[z[j]];
+ for (j = 0; j < g->len; ++j) d[k++] = dl[j];
}
} // FIXME: to add GL
}
}
return 0;
}
+/* FIXME: this function will fail given AB:GTX:GT. BCFtools never
+ * produces such FMT, but others may do. */
+int bcf_fix_gt(bcf1_t *b)
+{
+ char *s;
+ int i;
+ uint32_t tmp;
+ bcf_ginfo_t gt;
+ // check the presence of the GT FMT
+ if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
+ if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
+ tmp = bcf_str2int("GT", 2);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
+ gt = b->gi[i];
+ // move GT to the first
+ for (; i > 0; --i) b->gi[i] = b->gi[i-1];
+ b->gi[0] = gt;
+ memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
+ b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
+ return 0;
+}
+
+int bcf_fix_pl(bcf1_t *b)
+{
+ int i;
+ uint32_t tmp;
+ uint8_t *PL, *swap;
+ bcf_ginfo_t *gi;
+ // pinpoint PL
+ tmp = bcf_str2int("PL", 2);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ if (i == b->n_gi) return 0;
+ // prepare
+ gi = b->gi + i;
+ PL = (uint8_t*)gi->data;
+ swap = alloca(gi->len);
+ // loop through individuals
+ for (i = 0; i < b->n_smpl; ++i) {
+ int k, l, x;
+ uint8_t *PLi = PL + i * gi->len;
+ memcpy(swap, PLi, gi->len);
+ for (k = x = 0; k < b->n_alleles; ++k)
+ for (l = k; l < b->n_alleles; ++l)
+ PLi[l*(l+1)/2 + k] = swap[x++];
+ }
+ return 0;
+}
+
+int bcf_smpl_covered(const bcf1_t *b)
+{
+ int i, j, n = 0;
+ uint32_t tmp;
+ bcf_ginfo_t *gi;
+ // pinpoint PL
+ tmp = bcf_str2int("PL", 2);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ if (i == b->n_gi) return 0;
+ // count how many samples having PL!=[0..0]
+ gi = b->gi + i;
+ for (i = 0; i < b->n_smpl; ++i) {
+ uint8_t *PLi = ((uint8_t*)gi->data) + i * gi->len;
+ for (j = 0; j < gi->len; ++j)
+ if (PLi[j]) break;
+ if (j < gi->len) ++n;
+ }
+ return n;
+}
+
+static void *locate_field(const bcf1_t *b, const char *fmt, int l)
+{
+ int i;
+ uint32_t tmp;
+ tmp = bcf_str2int(fmt, l);
+ for (i = 0; i < b->n_gi; ++i)
+ if (b->gi[i].fmt == tmp) break;
+ return i == b->n_gi? 0 : b->gi[i].data;
+}
+
+int bcf_anno_max(bcf1_t *b)
+{
+ int k, max_gq, max_sp, n_het;
+ kstring_t str;
+ uint8_t *gt, *gq;
+ int32_t *sp;
+ max_gq = max_sp = n_het = 0;
+ gt = locate_field(b, "GT", 2);
+ if (gt == 0) return -1;
+ gq = locate_field(b, "GQ", 2);
+ sp = locate_field(b, "SP", 2);
+ if (sp)
+ for (k = 0; k < b->n_smpl; ++k)
+ if (gt[k]&0x3f)
+ max_sp = max_sp > (int)sp[k]? max_sp : sp[k];
+ if (gq)
+ for (k = 0; k < b->n_smpl; ++k)
+ if (gt[k]&0x3f)
+ max_gq = max_gq > (int)gq[k]? max_gq : gq[k];
+ for (k = 0; k < b->n_smpl; ++k) {
+ int a1, a2;
+ a1 = gt[k]&7; a2 = gt[k]>>3&7;
+ if ((!a1 && a2) || (!a2 && a1)) { // a het
+ if (gq == 0) ++n_het;
+ else if (gq[k] >= 20) ++n_het;
+ }
+ }
+ if (n_het) max_sp -= (int)(4.343 * log(n_het) + .499);
+ if (max_sp < 0) max_sp = 0;
+ memset(&str, 0, sizeof(kstring_t));
+ if (*b->info) kputc(';', &str);
+ ksprintf(&str, "MXSP=%d;MXGQ=%d", max_sp, max_gq);
+ bcf_append_info(b, str.s, str.l);
+ free(str.s);
+ return 0;
+}
+
+// FIXME: only data are shuffled; the header is NOT
+int bcf_shuffle(bcf1_t *b, int seed)
+{
+ int i, j, *a;
+ if (seed > 0) srand48(seed);
+ a = malloc(b->n_smpl * sizeof(int));
+ for (i = 0; i < b->n_smpl; ++i) a[i] = i;
+ for (i = b->n_smpl; i > 1; --i) {
+ int tmp;
+ j = (int)(drand48() * i);
+ tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;
+ }
+ for (j = 0; j < b->n_gi; ++j) {
+ bcf_ginfo_t *gi = b->gi + j;
+ uint8_t *swap, *data = (uint8_t*)gi->data;
+ swap = malloc(gi->len * b->n_smpl);
+ for (i = 0; i < b->n_smpl; ++i)
+ memcpy(swap + gi->len * a[i], data + gi->len * i, gi->len);
+ free(gi->data);
+ gi->data = swap;
+ }
+ free(a);
+ return 0;
+}
+
+bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list)
+{
+ int i, ret, j;
+ khint_t k;
+ bcf_hdr_t *h;
+ khash_t(str2id) *hash;
+ kstring_t s;
+ s.l = s.m = 0; s.s = 0;
+ hash = kh_init(str2id);
+ for (i = 0; i < h0->n_smpl; ++i) {
+ k = kh_put(str2id, hash, h0->sns[i], &ret);
+ kh_val(hash, k) = i;
+ }
+ for (i = j = 0; i < n; ++i) {
+ k = kh_get(str2id, hash, samples[i]);
+ if (k != kh_end(hash)) {
+ list[j++] = kh_val(hash, k);
+ kputs(samples[i], &s); kputc('\0', &s);
+ }
+ }
+ if (j < n) fprintf(pysamerr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+ kh_destroy(str2id, hash);
+ h = calloc(1, sizeof(bcf_hdr_t));
+ *h = *h0;
+ h->ns = 0; h->sns = 0;
+ h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
+ h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
+ h->l_smpl = s.l; h->sname = s.s;
+ bcf_hdr_sync(h);
+ return h;
+}
+
+int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
+{
+ int i, j;
+ for (j = 0; j < b->n_gi; ++j) {
+ bcf_ginfo_t *gi = b->gi + j;
+ uint8_t *swap;
+ swap = malloc(gi->len * b->n_smpl);
+ for (i = 0; i < n_smpl; ++i)
+ memcpy(swap + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
+ free(gi->data);
+ gi->data = swap;
+ }
+ b->n_smpl = n_smpl;
+ return 0;
+}
#include "bcf.h"
#include "prob1.h"
#include "kstring.h"
-
-#include "khash.h"
-KHASH_SET_INIT_INT64(set64)
+#include "time.h"
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
#define VC_VARONLY 16
#define VC_VCFIN 32
#define VC_UNCOMP 64
-#define VC_HWE 128
#define VC_KEEPALT 256
#define VC_ACGT_ONLY 512
#define VC_QCALL 1024
#define VC_CALL_GT 2048
#define VC_ADJLD 4096
#define VC_NO_INDEL 8192
-#define VC_FOLDED 16384
+#define VC_ANNO_MAX 16384
+#define VC_FIX_PL 32768
+#define VC_EM 0x10000
typedef struct {
- int flag, prior_type, n1;
- char *fn_list, *prior_file;
- double theta, pref, indel_frac;
+ int flag, prior_type, n1, n_sub, *sublist, n_perm;
+ char *prior_file, **subsam, *fn_dict;
+ uint8_t *ploidy;
+ double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
+ void *bed;
} viewconf_t;
-khash_t(set64) *bcf_load_pos(const char *fn, bcf_hdr_t *_h)
-{
- void *str2id;
- gzFile fp;
- kstream_t *ks;
- int ret, dret, lineno = 1;
- kstring_t *str;
- khash_t(set64) *hash = 0;
-
- hash = kh_init(set64);
- str2id = bcf_build_refhash(_h);
- str = calloc(1, sizeof(kstring_t));
- fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
- ks = ks_init(fp);
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
- int tid = bcf_str2id(str2id, str->s);
- if (tid >= 0 && dret != '\n') {
- if (ks_getuntil(ks, 0, str, &dret) >= 0) {
- uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
- kh_put(set64, hash, x, &ret);
- } else break;
- } else fprintf(pysamerr, "[%s] %s is not a reference name (line %d).\n", __func__, str->s, lineno);
- if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
- if (dret < 0) break;
- ++lineno;
- }
- bcf_str2id_destroy(str2id);
- ks_destroy(ks);
- gzclose(fp);
- free(str->s); free(str);
- return hash;
-}
-
-static double test_hwe(const double g[3])
-{
- extern double kf_gammaq(double p, double x);
- double fexp, chi2, f[3], n;
- int i;
- n = g[0] + g[1] + g[2];
- fexp = (2. * g[2] + g[1]) / (2. * n);
- if (fexp > 1. - 1e-10) fexp = 1. - 1e-10;
- if (fexp < 1e-10) fexp = 1e-10;
- f[0] = n * (1. - fexp) * (1. - fexp);
- f[1] = n * 2. * fexp * (1. - fexp);
- f[2] = n * fexp * fexp;
- for (i = 0, chi2 = 0.; i < 3; ++i)
- chi2 += (g[i] - f[i]) * (g[i] - f[i]) / f[i];
- return kf_gammaq(.5, chi2 / 2.);
-}
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
typedef struct {
double p[4];
bcf_sync(b);
}
-static int update_bcf1(int n_smpl, bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag)
+static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[9])
{
kstring_t s;
- int is_var = (pr->p_ref < pref);
- double p_hwe, r = is_var? pr->p_ref : 1. - pr->p_ref;
+ int has_I16, is_var;
+ double fq, r;
anno16_t a;
- p_hwe = pr->g[0] >= 0.? test_hwe(pr->g) : 1.0; // only do HWE g[] is calculated
- test16(b, &a);
- rm_info(b, "I16=");
+ has_I16 = test16(b, &a) >= 0? 1 : 0;
+ rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
kputs(b->info, &s);
if (b->info[0]) kputc(';', &s);
-// ksprintf(&s, "AF1=%.4lg;AFE=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, 1.-pr->f_exp, pr->cil, pr->cih);
- ksprintf(&s, "AF1=%.4lg;CI95=%.4lg,%.4lg", 1.-pr->f_em, pr->cil, pr->cih);
- ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
- if (a.is_tested) {
- if (pr->pc[0] >= 0.) ksprintf(&s, ";PC4=%lg,%lg,%lg,%lg", pr->pc[0], pr->pc[1], pr->pc[2], pr->pc[3]);
- ksprintf(&s, ";PV4=%.2lg,%.2lg,%.2lg,%.2lg", a.p[0], a.p[1], a.p[2], a.p[3]);
+ { // print EM
+ if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
+ if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
+ if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
+ if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
}
- if (pr->g[0] >= 0. && p_hwe <= .2)
- ksprintf(&s, ";GC=%.2lf,%.2lf,%.2lf;HWE=%.3lf", pr->g[2], pr->g[1], pr->g[0], p_hwe);
+ if (pr == 0) { // if pr is unset, return
+ kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+ return 1;
+ }
+
+ is_var = (pr->p_ref < pref);
+ r = is_var? pr->p_ref : pr->p_var;
+
+ ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
+ if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
+ if (fq < -999) fq = -999;
+ if (fq > 999) fq = 999;
+ ksprintf(&s, ";FQ=%.3g", fq);
+ if (pr->cmp[0] >= 0.) { // two sample groups
+ int i, q[3];
+ for (i = 1; i < 3; ++i) {
+ double x = pr->cmp[i] + pr->cmp[0]/2.;
+ q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
+ if (q[i] > 255) q[i] = 255;
+ }
+ if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
+ ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
+ }
+ if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
kputc('\0', &s);
kputs(b->fmt, &s); kputc('\0', &s);
free(b->str);
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
- b->qual = r < 1e-100? 99 : -4.343 * log(r);
- if (b->qual > 99) b->qual = 99;
+ b->qual = r < 1e-100? 999 : -4.343 * log(r);
+ if (b->qual > 999) b->qual = 999;
bcf_sync(b);
if (!is_var) bcf_shrink_alt(b, 1);
else if (!(flag&VC_KEEPALT))
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
bcf_sync(b);
for (i = 0; i < b->n_smpl; ++i) {
- x = bcf_p1_call_gt(pa, pr->f_em, i);
+ x = bcf_p1_call_gt(pa, pr->f_exp, i);
((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
}
return is_var;
}
-double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+static char **read_samples(const char *fn, int *_n)
+{
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s;
+ int dret, n = 0, max = 0;
+ char **sam = 0;
+ *_n = 0;
+ s.l = s.m = 0; s.s = 0;
+ fp = gzopen(fn, "r");
+ if (fp == 0) return 0; // fail to open file
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ int l;
+ if (max == n) {
+ max = max? max<<1 : 4;
+ sam = realloc(sam, sizeof(void*)*max);
+ }
+ l = s.l;
+ sam[n] = malloc(s.l + 2);
+ strcpy(sam[n], s.s);
+ sam[n][l+1] = 2; // by default, diploid
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
+ int x = (int)s.s[0] - '0';
+ if (x == 1 || x == 2) sam[n][l+1] = x;
+ else fprintf(pysamerr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
+ }
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ++n;
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(s.s);
+ *_n = n;
+ return sam;
+}
+
+static void write_header(bcf_hdr_t *h)
+{
+ kstring_t str;
+ str.l = h->l_txt? h->l_txt - 1 : 0;
+ str.m = str.l + 1; str.s = h->txt;
+ if (!strstr(str.s, "##INFO=<ID=DP,"))
+ kputs("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=DP4,"))
+ kputs("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=MQ,"))
+ kputs("##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Root-mean-square mapping quality of covering reads\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=FQ,"))
+ kputs("##INFO=<ID=FQ,Number=1,Type=Float,Description=\"Phred probability of all samples being the same\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AF1,"))
+ kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the site allele frequency of the first ALT allele\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=G3,"))
+ kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=HWE,"))
+ kputs("##INFO=<ID=HWE,Number=1,Type=Float,Description=\"Chi^2 based HWE test P-value based on G3\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=CI95,"))
+ kputs("##INFO=<ID=CI95,Number=2,Type=Float,Description=\"Equal-tail Bayesian credible interval of the site allele frequency at the 95% level\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PV4,"))
+ kputs("##INFO=<ID=PV4,Number=4,Type=Float,Description=\"P-values for strand bias, baseQ bias, mapQ bias and tail distance bias\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=INDEL,"))
+ kputs("##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PC2,"))
+ kputs("##INFO=<ID=PC2,Number=2,Type=Integer,Description=\"Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=PCHI2,"))
+ kputs("##INFO=<ID=PCHI2,Number=1,Type=Float,Description=\"Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=QCHI2,"))
+ kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=RP,"))
+ kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GT,"))
+ kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
+ kputs("##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=GL,"))
+ kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=DP,"))
+ kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=SP,"))
+ kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=PL,"))
+ kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
+ h->l_txt = str.l + 1; h->txt = str.s;
+}
+
+double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
int bcfview(int argc, char *argv[])
{
extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
+ extern int bcf_fix_gt(bcf1_t *b);
+ extern int bcf_anno_max(bcf1_t *b);
+ extern int bcf_shuffle(bcf1_t *b, int seed);
bcf_t *bp, *bout = 0;
bcf1_t *b, *blast;
- int c;
+ int c, *seeds = 0;
uint64_t n_processed = 0;
viewconf_t vc;
bcf_p1aux_t *p1 = 0;
- bcf_hdr_t *h;
+ bcf_hdr_t *hin, *hout;
int tid, begin, end;
char moder[4], modew[4];
- khash_t(set64) *hash = 0;
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
- vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.;
- while ((c = getopt(argc, argv, "fN1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
+ vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:")) >= 0) {
switch (c) {
- case 'f': vc.flag |= VC_FOLDED; break;
case '1': vc.n1 = atoi(optarg); break;
- case 'l': vc.fn_list = strdup(optarg); break;
+ case 'l': vc.bed = bed_read(optarg); break;
+ case 'D': vc.fn_dict = strdup(optarg); break;
+ case 'F': vc.flag |= VC_FIX_PL; break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
case 'G': vc.flag |= VC_NO_GENO; break;
case 'A': vc.flag |= VC_KEEPALT; break;
case 'b': vc.flag |= VC_BCFOUT; break;
case 'S': vc.flag |= VC_VCFIN; break;
case 'c': vc.flag |= VC_CALL; break;
+ case 'e': vc.flag |= VC_EM; break;
case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
- case 'H': vc.flag |= VC_HWE; break;
case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
case 'I': vc.flag |= VC_NO_INDEL; break;
+ case 'M': vc.flag |= VC_ANNO_MAX; break;
case 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
case 'i': vc.indel_frac = atof(optarg); break;
case 'Q': vc.flag |= VC_QCALL; break;
case 'L': vc.flag |= VC_ADJLD; break;
+ case 'U': vc.n_perm = atoi(optarg); break;
+ case 'C': vc.min_lrt = atof(optarg); break;
+ case 'X': vc.min_perm_p = atof(optarg); break;
+ case 'd': vc.min_smpl_frac = atof(optarg); break;
+ case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
+ vc.ploidy = calloc(vc.n_sub + 1, 1);
+ for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
+ tid = -1;
+ break;
case 'P':
if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
}
if (argc == optind) {
fprintf(pysamerr, "\n");
- fprintf(pysamerr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
- fprintf(pysamerr, "Options: -c SNP calling\n");
- fprintf(pysamerr, " -v output potential variant sites only (force -c)\n");
- fprintf(pysamerr, " -g call genotypes at variant sites (force -c)\n");
- fprintf(pysamerr, " -b output BCF instead of VCF\n");
- fprintf(pysamerr, " -u uncompressed BCF output (force -b)\n");
- fprintf(pysamerr, " -S input is VCF\n");
- fprintf(pysamerr, " -A keep all possible alternate alleles at variant sites\n");
- fprintf(pysamerr, " -G suppress all individual genotype information\n");
- fprintf(pysamerr, " -H perform Hardy-Weinberg test (slower)\n");
- fprintf(pysamerr, " -N skip sites where REF is not A/C/G/T\n");
- fprintf(pysamerr, " -Q output the QCALL likelihood format\n");
- fprintf(pysamerr, " -L calculate LD for adjacent sites\n");
- fprintf(pysamerr, " -I skip indels\n");
- fprintf(pysamerr, " -f reference-free variant calling\n");
- fprintf(pysamerr, " -1 INT number of group-1 samples [0]\n");
- fprintf(pysamerr, " -l FILE list of sites to output [all sites]\n");
- fprintf(pysamerr, " -t FLOAT scaled substitution mutation rate [%.4lg]\n", vc.theta);
- fprintf(pysamerr, " -i FLOAT indel-to-substitution ratio [%.4lg]\n", vc.indel_frac);
- fprintf(pysamerr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3lg]\n", vc.pref);
- fprintf(pysamerr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(pysamerr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
+ fprintf(pysamerr, "Input/output options:\n\n");
+ fprintf(pysamerr, " -A keep all possible alternate alleles at variant sites\n");
+ fprintf(pysamerr, " -b output BCF instead of VCF\n");
+ fprintf(pysamerr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
+ fprintf(pysamerr, " -F PL generated by r921 or before (which generate old ordering)\n");
+ fprintf(pysamerr, " -G suppress all individual genotype information\n");
+ fprintf(pysamerr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n");
+ fprintf(pysamerr, " -L calculate LD for adjacent sites\n");
+ fprintf(pysamerr, " -N skip sites where REF is not A/C/G/T\n");
+ fprintf(pysamerr, " -Q output the QCALL likelihood format\n");
+ fprintf(pysamerr, " -s FILE list of samples to use [all samples]\n");
+ fprintf(pysamerr, " -S input is VCF\n");
+ fprintf(pysamerr, " -u uncompressed BCF output (force -b)\n");
+ fprintf(pysamerr, "\nConsensus/variant calling options:\n\n");
+ fprintf(pysamerr, " -c SNP calling (force -e)\n");
+ fprintf(pysamerr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
+ fprintf(pysamerr, " -e likelihood based analyses\n");
+ fprintf(pysamerr, " -g call genotypes at variant sites (force -c)\n");
+ fprintf(pysamerr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
+ fprintf(pysamerr, " -I skip indels\n");
+ fprintf(pysamerr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
+ fprintf(pysamerr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(pysamerr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
+ fprintf(pysamerr, " -v output potential variant sites only (force -c)\n");
+ fprintf(pysamerr, "\nContrast calling and association test options:\n\n");
+ fprintf(pysamerr, " -1 INT number of group-1 samples [0]\n");
+ fprintf(pysamerr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
+ fprintf(pysamerr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
+ fprintf(pysamerr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);
fprintf(pysamerr, "\n");
return 1;
}
+ if (vc.flag & VC_CALL) vc.flag |= VC_EM;
+ if ((vc.flag & VC_VCFIN) && (vc.flag & VC_BCFOUT) && vc.fn_dict == 0) {
+ fprintf(pysamerr, "[%s] For VCF->BCF conversion please specify the sequence dictionary with -D\n", __func__);
+ return 1;
+ }
+ if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
+ if (vc.n_perm > 0) {
+ seeds = malloc(vc.n_perm * sizeof(int));
+ srand48(time(0));
+ for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
+ }
b = calloc(1, sizeof(bcf1_t));
blast = calloc(1, sizeof(bcf1_t));
strcpy(moder, "r");
if (vc.flag & VC_BCFOUT) strcat(modew, "b");
if (vc.flag & VC_UNCOMP) strcat(modew, "u");
bp = vcf_open(argv[optind], moder);
- h = vcf_hdr_read(bp);
+ hin = hout = vcf_hdr_read(bp);
+ if (vc.fn_dict && (vc.flag & VC_VCFIN))
+ vcf_dictread(bp, hin, vc.fn_dict);
bout = vcf_open("-", modew);
- if (!(vc.flag & VC_QCALL)) vcf_hdr_write(bout, h);
+ if (!(vc.flag & VC_QCALL)) {
+ if (vc.n_sub) {
+ vc.sublist = calloc(vc.n_sub, sizeof(int));
+ hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
+ }
+ if (vc.flag & VC_CALL) write_header(hout);
+ vcf_hdr_write(bout, hout);
+ }
if (vc.flag & VC_CALL) {
- p1 = bcf_p1_init(h->n_smpl);
+ p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
if (vc.prior_file) {
if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
fprintf(pysamerr, "[%s] fail to read the prior AFS.\n", __func__);
return 1;
}
} else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
- if (vc.n1 > 0) {
+ if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
bcf_p1_set_n1(p1, vc.n1);
bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
}
if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
- if (vc.flag & VC_FOLDED) bcf_p1_set_folded(p1);
}
- if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
- void *str2id = bcf_build_refhash(h);
+ void *str2id = bcf_build_refhash(hout);
if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
bcf_idx_t *idx;
idx = bcf_idx_load(argv[optind]);
}
}
}
- while (vcf_read(bp, h, b) > 0) {
- int is_indel = bcf_is_indel(b);
+ while (vcf_read(bp, hin, b) > 0) {
+ int is_indel;
+ double em[9];
+ if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
+ if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
+ extern int bcf_smpl_covered(const bcf1_t *b);
+ int n = bcf_smpl_covered(b);
+ if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
+ }
+ if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
+ if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
+ is_indel = bcf_is_indel(b);
if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
int x;
x = toupper(b->ref[0]);
if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
}
- if (hash) {
- uint64_t x = (uint64_t)b->tid<<32 | b->pos;
- khint_t k = kh_get(set64, hash, x);
- if (kh_size(hash) == 0) break;
- if (k == kh_end(hash)) continue;
- kh_del(set64, hash, k);
- }
+ if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
if (tid >= 0) {
int l = strlen(b->ref);
l = b->pos + (l > 0? l : 1);
}
++n_processed;
if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
- bcf_2qcall(h, b);
+ bcf_2qcall(hout, b);
continue;
}
+ if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0xff, em);
+ else {
+ int i;
+ for (i = 0; i < 9; ++i) em[i] = -1.;
+ }
if (vc.flag & (VC_CALL|VC_ADJLD)) bcf_gl2pl(b);
if (vc.flag & VC_CALL) { // call variants
bcf_p1rst_t pr;
- bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here
- if (vc.flag&VC_HWE) bcf_p1_cal_g3(p1, pr.g);
+ int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
if (n_processed % 100000 == 0) {
fprintf(pysamerr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
bcf_p1_dump_afs(p1);
}
if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
- update_bcf1(h->n_smpl, b, p1, &pr, vc.pref, vc.flag);
- }
+ if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
+ bcf_p1rst_t r;
+ int i, n = 0;
+ for (i = 0; i < vc.n_perm; ++i) {
+#ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
+ double x[9];
+ bcf_shuffle(b, seeds[i]);
+ bcf_em1(b, vc.n1, 1<<7, x);
+ if (x[7] < em[7]) ++n;
+#else
+ bcf_shuffle(b, seeds[i]);
+ bcf_p1_cal(b, 1, p1, &r);
+ if (pr.p_chi2 >= r.p_chi2) ++n;
+#endif
+ }
+ pr.perm_rank = n;
+ }
+ if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em);
+ } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em);
if (vc.flag & VC_ADJLD) { // compute LD
double f[4], r2;
- if ((r2 = bcf_ld_freq(blast, b, f)) >= 0) {
+ if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
kstring_t s;
s.m = s.l = 0; s.s = 0;
if (*b->info) kputc(';', &s);
- ksprintf(&s, "NEIR=%.3lf;NEIF=%.3lf,%.3lf", r2, f[0]+f[2], f[0]+f[1]);
+ ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
bcf_append_info(b, s.s, s.l);
free(s.s);
}
bcf_cpy(blast, b);
}
+ if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
if (vc.flag & VC_NO_GENO) { // do not output GENO fields
b->n_gi = 0;
b->fmt[0] = '\0';
- }
- vcf_write(bout, h, b);
+ b->l_str = b->fmt - b->str + 1;
+ } else bcf_fix_gt(b);
+ vcf_write(bout, hout, b);
}
if (vc.prior_file) free(vc.prior_file);
if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
- bcf_hdr_destroy(h);
+ if (hin != hout) bcf_hdr_destroy(hout);
+ bcf_hdr_destroy(hin);
bcf_destroy(b); bcf_destroy(blast);
vcf_close(bp); vcf_close(bout);
- if (hash) kh_destroy(set64, hash);
- if (vc.fn_list) free(vc.fn_list);
+ if (vc.fn_dict) free(vc.fn_dict);
+ if (vc.ploidy) free(vc.ploidy);
+ if (vc.n_sub) {
+ int i;
+ for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
+ free(vc.subsam); free(vc.sublist);
+ }
+ if (vc.bed) bed_destroy(vc.bed);
+ if (seeds) free(seeds);
if (p1) bcf_p1_destroy(p1);
return 0;
}
--- /dev/null
+#include "pysam.h"
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "bcf.h"
+#include "kmin.h"
+
+static double g_q2p[256];
+
+#define ITER_MAX 50
+#define ITER_TRY 10
+#define EPS 1e-5
+
+extern double kf_gammaq(double, double);
+
+/*
+ Generic routines
+ */
+// get the 3 genotype likelihoods
+static double *get_pdg3(const bcf1_t *b)
+{
+ double *pdg;
+ const uint8_t *PL = 0;
+ int i, PL_len = 0;
+ // initialize g_q2p if necessary
+ if (g_q2p[0] == 0.)
+ for (i = 0; i < 256; ++i)
+ g_q2p[i] = pow(10., -i / 10.);
+ // set PL and PL_len
+ for (i = 0; i < b->n_gi; ++i) {
+ if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ PL = (const uint8_t*)b->gi[i].data;
+ PL_len = b->gi[i].len;
+ break;
+ }
+ }
+ if (i == b->n_gi) return 0; // no PL
+ // fill pdg
+ pdg = malloc(3 * b->n_smpl * sizeof(double));
+ for (i = 0; i < b->n_smpl; ++i) {
+ const uint8_t *pi = PL + i * PL_len;
+ double *p = pdg + i * 3;
+ p[0] = g_q2p[pi[2]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]];
+ }
+ return pdg;
+}
+
+// estimate site allele frequency in a very naive and inaccurate way
+static double est_freq(int n, const double *pdg)
+{
+ int i, gcnt[3], tmp1;
+ // get a rough estimate of the genotype frequency
+ gcnt[0] = gcnt[1] = gcnt[2] = 0;
+ for (i = 0; i < n; ++i) {
+ const double *p = pdg + i * 3;
+ if (p[0] != 1. || p[1] != 1. || p[2] != 1.) {
+ int which = p[0] > p[1]? 0 : 1;
+ which = p[which] > p[2]? which : 2;
+ ++gcnt[which];
+ }
+ }
+ tmp1 = gcnt[0] + gcnt[1] + gcnt[2];
+ return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1;
+}
+
+/*
+ Single-locus EM
+ */
+
+typedef struct {
+ int beg, end;
+ const double *pdg;
+} minaux1_t;
+
+static double prob1(double f, void *data)
+{
+ minaux1_t *a = (minaux1_t*)data;
+ double p = 1., l = 0., f3[3];
+ int i;
+// printf("brent %lg\n", f);
+ if (f < 0 || f > 1) return 1e300;
+ f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f;
+ for (i = a->beg; i < a->end; ++i) {
+ const double *pdg = a->pdg + i * 3;
+ p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
+ if (p < 1e-200) l -= log(p), p = 1.;
+ }
+ return l - log(p);
+}
+
+// one EM iteration for allele frequency estimate
+static double freq_iter(double *f, const double *_pdg, int beg, int end)
+{
+ double f0 = *f, f3[3], err;
+ int i;
+// printf("em %lg\n", *f);
+ f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+ for (i = beg, f0 = 0.; i < end; ++i) {
+ const double *pdg = _pdg + i * 3;
+ f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
+ / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
+ }
+ f0 /= (end - beg) * 2;
+ err = fabs(f0 - *f);
+ *f = f0;
+ return err;
+}
+
+/* The following function combines EM and Brent's method. When the signal from
+ * the data is strong, EM is faster but sometimes, EM may converge very slowly.
+ * When this happens, we switch to Brent's method. The idea is learned from
+ * Rasmus Nielsen.
+ */
+static double freqml(double f0, int beg, int end, const double *pdg)
+{
+ int i;
+ double f;
+ for (i = 0, f = f0; i < ITER_TRY; ++i)
+ if (freq_iter(&f, pdg, beg, end) < EPS) break;
+ if (i == ITER_TRY) { // haven't converged yet; try Brent's method
+ minaux1_t a;
+ a.beg = beg; a.end = end; a.pdg = pdg;
+ kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f);
+ }
+ return f;
+}
+
+// one EM iteration for genotype frequency estimate
+static double g3_iter(double g[3], const double *_pdg, int beg, int end)
+{
+ double err, gg[3];
+ int i;
+ gg[0] = gg[1] = gg[2] = 0.;
+// printf("%lg,%lg,%lg\n", g[0], g[1], g[2]);
+ for (i = beg; i < end; ++i) {
+ double sum, tmp[3];
+ const double *pdg = _pdg + i * 3;
+ tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2];
+ sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg);
+ gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum;
+ }
+ err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]);
+ err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]);
+ g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2];
+ return err;
+}
+
+// perform likelihood ratio test
+static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3])
+{
+ double r;
+ int i;
+ for (i = 0, r = 1.; i < n1; ++i) {
+ const double *p = pdg + i * 3;
+ r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2])
+ / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+ }
+ for (; i < n; ++i) {
+ const double *p = pdg + i * 3;
+ r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2])
+ / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
+ }
+ return r;
+}
+
+// x[0]: ref frequency
+// x[1..3]: alt-alt, alt-ref, ref-ref frequenc
+// x[4]: HWE P-value
+// x[5..6]: group1 freq, group2 freq
+// x[7]: 1-degree P-value
+// x[8]: 2-degree P-value
+int bcf_em1(const bcf1_t *b, int n1, int flag, double x[9])
+{
+ double *pdg;
+ int i, n, n2;
+ if (b->n_alleles < 2) return -1; // one allele only
+ // initialization
+ if (n1 < 0 || n1 > b->n_smpl) n1 = 0;
+ if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required
+ if (flag & 0xf<<1) flag |= 0xf<<1;
+ n = b->n_smpl; n2 = n - n1;
+ pdg = get_pdg3(b);
+ if (pdg == 0) return -1;
+ for (i = 0; i < 9; ++i) x[i] = -1.;
+ {
+ if ((x[0] = est_freq(n, pdg)) < 0.) {
+ free(pdg);
+ return -1; // no data
+ }
+ x[0] = freqml(x[0], 0, n, pdg);
+ }
+ if (flag & (0xf<<1|1<<8)) { // estimate the genotype frequency and test HWE
+ double *g = x + 1, f3[3], r;
+ f3[0] = g[0] = (1 - x[0]) * (1 - x[0]);
+ f3[1] = g[1] = 2 * x[0] * (1 - x[0]);
+ f3[2] = g[2] = x[0] * x[0];
+ for (i = 0; i < ITER_MAX; ++i)
+ if (g3_iter(g, pdg, 0, n) < EPS) break;
+ // Hardy-Weinberg equilibrium (HWE)
+ for (i = 0, r = 1.; i < n; ++i) {
+ double *p = pdg + i * 3;
+ r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]);
+ }
+ x[4] = kf_gammaq(.5, log(r));
+ }
+ if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency
+ x[5] = freqml(x[0], 0, n1, pdg);
+ x[6] = freqml(x[0], n1, n, pdg);
+ }
+ if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value
+ double f[3], f3[3][3];
+ f[0] = x[0]; f[1] = x[5]; f[2] = x[6];
+ for (i = 0; i < 3; ++i)
+ f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i];
+ x[7] = kf_gammaq(.5, log(lk_ratio_test(n, n1, pdg, f3)));
+ }
+ if ((flag & 1<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
+ double g[3][3];
+ for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double));
+ for (i = 0; i < ITER_MAX; ++i)
+ if (g3_iter(g[1], pdg, 0, n1) < EPS) break;
+ for (i = 0; i < ITER_MAX; ++i)
+ if (g3_iter(g[2], pdg, n1, n) < EPS) break;
+ x[8] = kf_gammaq(1., log(lk_ratio_test(n, n1, pdg, g)));
+ }
+ // free
+ free(pdg);
+ return 0;
+}
+
+/*
+ Two-locus EM (LD)
+ */
+
+#define _G1(h, k) ((h>>1&1) + (k>>1&1))
+#define _G2(h, k) ((h&1) + (k&1))
+
+// 0: the previous site; 1: the current site
+static int pair_freq_iter(int n, double *pdg[2], double f[4])
+{
+ double ff[4];
+ int i, k, h;
+// printf("%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]);
+ memset(ff, 0, 4 * sizeof(double));
+ for (i = 0; i < n; ++i) {
+ double *p[2], sum, tmp;
+ p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
+ for (k = 0, sum = 0.; k < 4; ++k)
+ for (h = 0; h < 4; ++h)
+ sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
+ for (k = 0; k < 4; ++k) {
+ tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
+ + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
+ + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
+ + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
+ ff[k] += f[k] * tmp / sum;
+ }
+ }
+ for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
+ return 0;
+}
+
+double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
+{
+ const bcf1_t *b[2];
+ int i, j, n_smpl;
+ double *pdg[2], flast[4], r, f0[2];
+ // initialize others
+ if (b0->n_smpl != b1->n_smpl) return -1; // different number of samples
+ n_smpl = b0->n_smpl;
+ b[0] = b0; b[1] = b1;
+ f[0] = f[1] = f[2] = f[3] = -1.;
+ if (b[0]->n_alleles < 2 || b[1]->n_alleles < 2) return -1; // one allele only
+ pdg[0] = get_pdg3(b0); pdg[1] = get_pdg3(b1);
+ if (pdg[0] == 0 || pdg[1] == 0) {
+ free(pdg[0]); free(pdg[1]);
+ return -1;
+ }
+ // set the initial value
+ f0[0] = est_freq(n_smpl, pdg[0]);
+ f0[1] = est_freq(n_smpl, pdg[1]);
+ f[0] = (1 - f0[0]) * (1 - f0[1]); f[3] = f0[0] * f0[1];
+ f[1] = (1 - f0[0]) * f0[1]; f[2] = f0[0] * (1 - f0[1]);
+ // iteration
+ for (j = 0; j < ITER_MAX; ++j) {
+ double eps = 0;
+ memcpy(flast, f, 4 * sizeof(double));
+ pair_freq_iter(n_smpl, pdg, f);
+ for (i = 0; i < 4; ++i) {
+ double x = fabs(f[i] - flast[i]);
+ if (x > eps) eps = x;
+ }
+ if (eps < EPS) break;
+ }
+ // free
+ free(pdg[0]); free(pdg[1]);
+ { // calculate r^2
+ double p[2], q[2], D;
+ p[0] = f[0] + f[1]; q[0] = 1 - p[0];
+ p[1] = f[0] + f[2]; q[1] = 1 - p[1];
+ D = f[0] * f[3] - f[1] * f[2];
+ r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
+// printf("R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r);
+ if (isnan(r)) r = -1.;
+ }
+ return r;
+}
n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n
max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail
- min = (n1_ + n_1 - n < 0) ? 0 : (n1_ + n_1 - n < 0); // min n11, for left tail
+ min = n1_ + n_1 - n;
+ if (min < 0) min = 0; // min n11, for left tail
*two = *_left = *_right = 1.;
if (min == max) return 1.; // no need to do test
q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table
p = hypergeo_acc(max, 0, 0, 0, &aux);
for (right = 0., j = max - 1; p < 0.99999999 * q; --j) // loop until underflow
right += p, p = hypergeo_acc(j, 0, 0, 0, &aux);
+ ++j;
if (p < 1.00000001 * q) right += p;
else ++j;
// two-tail
--- /dev/null
+#include "pysam.h"
+
+/* The MIT License
+
+ Copyright (c) 2008, 2010 by Attractive Chaos <attractor@live.co.uk>
+
+ 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.
+*/
+
+/* Hooke-Jeeves algorithm for nonlinear minimization
+
+ Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and
+ the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the
+ papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM
+ 6(6):313-314). The original algorithm was designed by Hooke and
+ Jeeves (ACM 8:212-229). This program is further revised according to
+ Johnson's implementation at Netlib (opt/hooke.c).
+
+ Hooke-Jeeves algorithm is very simple and it works quite well on a
+ few examples. However, it might fail to converge due to its heuristic
+ nature. A possible improvement, as is suggested by Johnson, may be to
+ choose a small r at the beginning to quickly approach to the minimum
+ and a large r at later step to hit the minimum.
+ */
+
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "kmin.h"
+
+static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls)
+{
+ int k, j = *n_calls;
+ double ftmp;
+ for (k = 0; k != n; ++k) {
+ x1[k] += dx[k];
+ ftmp = func(n, x1, data); ++j;
+ if (ftmp < fx1) fx1 = ftmp;
+ else { /* search the opposite direction */
+ dx[k] = 0.0 - dx[k];
+ x1[k] += dx[k] + dx[k];
+ ftmp = func(n, x1, data); ++j;
+ if (ftmp < fx1) fx1 = ftmp;
+ else x1[k] -= dx[k]; /* back to the original x[k] */
+ }
+ }
+ *n_calls = j;
+ return fx1; /* here: fx1=f(n,x1) */
+}
+
+double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls)
+{
+ double fx, fx1, *x1, *dx, radius;
+ int k, n_calls = 0;
+ x1 = (double*)calloc(n, sizeof(double));
+ dx = (double*)calloc(n, sizeof(double));
+ for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */
+ dx[k] = fabs(x[k]) * r;
+ if (dx[k] == 0) dx[k] = r;
+ }
+ radius = r;
+ fx1 = fx = func(n, x, data); ++n_calls;
+ for (;;) {
+ memcpy(x1, x, n * sizeof(double)); /* x1 = x */
+ fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls);
+ while (fx1 < fx) {
+ for (k = 0; k != n; ++k) {
+ double t = x[k];
+ dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]);
+ x[k] = x1[k];
+ x1[k] = x1[k] + x1[k] - t;
+ }
+ fx = fx1;
+ if (n_calls >= max_calls) break;
+ fx1 = func(n, x1, data); ++n_calls;
+ fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls);
+ if (fx1 >= fx) break;
+ for (k = 0; k != n; ++k)
+ if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break;
+ if (k == n) break;
+ }
+ if (radius >= eps) {
+ if (n_calls >= max_calls) break;
+ radius *= r;
+ for (k = 0; k != n; ++k) dx[k] *= r;
+ } else break; /* converge */
+ }
+ free(x1); free(dx);
+ return fx1;
+}
+
+// I copied this function somewhere several years ago with some of my modifications, but I forgot the source.
+double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin)
+{
+ double bound, u, r, q, fu, tmp, fa, fb, fc, c;
+ const double gold1 = 1.6180339887;
+ const double gold2 = 0.3819660113;
+ const double tiny = 1e-20;
+ const int max_iter = 100;
+
+ double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw;
+ int iter;
+
+ fa = func(a, data); fb = func(b, data);
+ if (fb > fa) { // swap, such that f(a) > f(b)
+ tmp = a; a = b; b = tmp;
+ tmp = fa; fa = fb; fb = tmp;
+ }
+ c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation
+ while (fb > fc) {
+ bound = b + 100.0 * (c - b); // the farthest point where we want to go
+ r = (b - a) * (fb - fc);
+ q = (b - c) * (fb - fa);
+ if (fabs(q - r) < tiny) { // avoid 0 denominator
+ tmp = q > r? tiny : 0.0 - tiny;
+ } else tmp = q - r;
+ u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point
+ if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c
+ fu = func(u, data);
+ if (fu < fc) { // (b,u,c) bracket the minimum
+ a = b; b = u; fa = fb; fb = fu;
+ break;
+ } else if (fu > fb) { // (a,b,u) bracket the minimum
+ c = u; fc = fu;
+ break;
+ }
+ u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation
+ } else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound
+ fu = func(u, data);
+ if (fu < fc) { // fb > fc > fu
+ b = c; c = u; u = c + gold1 * (c - b);
+ fb = fc; fc = fu; fu = func(u, data);
+ } else { // (b,c,u) bracket the minimum
+ a = b; b = c; c = u;
+ fa = fb; fb = fc; fc = fu;
+ break;
+ }
+ } else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound
+ u = bound; fu = func(u, data);
+ } else { // u goes the other way around, use golden section extrapolation
+ u = c + gold1 * (c - b); fu = func(u, data);
+ }
+ a = b; b = c; c = u;
+ fa = fb; fb = fc; fc = fu;
+ }
+ if (a > c) u = a, a = c, c = u; // swap
+
+ // now, a<b<c, fa>fb and fb<fc, move on to Brent's algorithm
+ e = d = 0.0;
+ w = v = b; fv = fw = fb;
+ for (iter = 0; iter != max_iter; ++iter) {
+ mid = 0.5 * (a + c);
+ tol2 = 2.0 * (tol1 = tol * fabs(b) + tiny);
+ if (fabs(b - mid) <= (tol2 - 0.5 * (c - a))) {
+ *xmin = b; return fb; // found
+ }
+ if (fabs(e) > tol1) {
+ // related to parabolic interpolation
+ r = (b - w) * (fb - fv);
+ q = (b - v) * (fb - fw);
+ p = (b - v) * q - (b - w) * r;
+ q = 2.0 * (q - r);
+ if (q > 0.0) p = 0.0 - p;
+ else q = 0.0 - q;
+ eold = e; e = d;
+ if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) {
+ d = gold2 * (e = (b >= mid ? a - b : c - b));
+ } else {
+ d = p / q; u = b + d; // actual parabolic interpolation happens here
+ if (u - a < tol2 || c - u < tol2)
+ d = (mid > b)? tol1 : 0.0 - tol1;
+ }
+ } else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation
+ u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1);
+ fu = func(u, data);
+ if (fu <= fb) { // u is the minimum point so far
+ if (u >= b) a = b;
+ else c = b;
+ v = w; w = b; b = u; fv = fw; fw = fb; fb = fu;
+ } else { // adjust (a,c) and (u,v,w)
+ if (u < b) a = u;
+ else c = u;
+ if (fu <= fw || w == b) {
+ v = w; w = u;
+ fv = fw; fw = fu;
+ } else if (fu <= fv || v == b || v == w) {
+ v = u; fv = fu;
+ }
+ }
+ }
+ *xmin = b;
+ return fb;
+}
--- /dev/null
+/*
+ Copyright (c) 2008, 2010 by Attractive Chaos <attractor@live.co.uk>
+
+ 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.
+*/
+
+#ifndef KMIN_H
+#define KMIN_H
+
+#define KMIN_RADIUS 0.5
+#define KMIN_EPS 1e-7
+#define KMIN_MAXCALL 50000
+
+typedef double (*kmin_f)(int, double*, void*);
+typedef double (*kmin1_f)(double, void*);
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+ double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls);
+ double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+++ /dev/null
-#include "pysam.h"
-
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include "bcf.h"
-
-static double g_q2p[256];
-
-#define LD_ITER_MAX 50
-#define LD_ITER_EPS 1e-4
-
-#define _G1(h, k) ((h>>1&1) + (k>>1&1))
-#define _G2(h, k) ((h&1) + (k&1))
-
-// 0: the previous site; 1: the current site
-static int freq_iter(int n, double *pdg[2], double f[4])
-{
- double ff[4];
- int i, k, h;
- memset(ff, 0, 4 * sizeof(double));
- for (i = 0; i < n; ++i) {
- double *p[2], sum, tmp;
- p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
- for (k = 0, sum = 0.; k < 4; ++k)
- for (h = 0; h < 4; ++h)
- sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
- for (k = 0; k < 4; ++k) {
- tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
- + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
- + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
- + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
- ff[k] += f[k] * tmp / sum;
- }
- }
- for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
- return 0;
-}
-
-double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
-{
- const bcf1_t *b[2];
- uint8_t *PL[2];
- int i, j, PL_len[2], n_smpl;
- double *pdg[2], flast[4], r;
- // initialize g_q2p if necessary
- if (g_q2p[0] == 0.)
- for (i = 0; i < 256; ++i)
- g_q2p[i] = pow(10., -i / 10.);
- // initialize others
- if (b0->n_smpl != b1->n_smpl) return -1; // different number of samples
- n_smpl = b0->n_smpl;
- b[0] = b0; b[1] = b1;
- f[0] = f[1] = f[2] = f[3] = -1.;
- if (b[0]->n_alleles < 2 || b[1]->n_alleles < 2) return -1; // one allele only
- // set PL and PL_len
- for (j = 0; j < 2; ++j) {
- const bcf1_t *bj = b[j];
- for (i = 0; i < bj->n_gi; ++i) {
- if (bj->gi[i].fmt == bcf_str2int("PL", 2)) {
- PL[j] = (uint8_t*)bj->gi[i].data;
- PL_len[j] = bj->gi[i].len;
- break;
- }
- }
- if (i == bj->n_gi) return -1; // no PL
- }
- // fill pdg[2]
- pdg[0] = malloc(3 * n_smpl * sizeof(double));
- pdg[1] = malloc(3 * n_smpl * sizeof(double));
- for (j = 0; j < 2; ++j) {
- for (i = 0; i < n_smpl; ++i) {
- const uint8_t *pi = PL[j] + i * PL_len[j];
- double *p = pdg[j] + i * 3;
- p[0] = g_q2p[pi[b[j]->n_alleles]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]];
- }
- }
- // iteration
- f[0] = f[1] = f[2] = f[3] = 0.25; // this is a really bad guess...
- for (j = 0; j < LD_ITER_MAX; ++j) {
- double eps = 0;
- memcpy(flast, f, 4 * sizeof(double));
- freq_iter(n_smpl, pdg, f);
- for (i = 0; i < 4; ++i) {
- double x = fabs(f[i] - flast[i]);
- if (x > eps) eps = x;
- }
- if (eps < LD_ITER_EPS) break;
- }
- // free
- free(pdg[0]); free(pdg[1]);
- { // calculate r^2
- double p[2], q[2], D;
- p[0] = f[0] + f[1]; q[0] = 1 - p[0];
- p[1] = f[0] + f[2]; q[1] = 1 - p[1];
- D = f[0] * f[3] - f[1] * f[2];
- r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
- // fprintf(pysamerr, "R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r2);
- if (isnan(r)) r = -1.;
- }
- return r;
-}
#include <string.h>
#include <stdio.h>
#include <errno.h>
+#include <assert.h>
#include "prob1.h"
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
#define MC_MAX_EM_ITER 16
-#define MC_EM_EPS 1e-4
+#define MC_EM_EPS 1e-5
#define MC_DEF_INDEL 0.15
unsigned char seq_nt4_table[256] = {
};
struct __bcf_p1aux_t {
- int n, M, n1, is_indel, is_folded;
+ int n, M, n1, is_indel;
+ uint8_t *ploidy; // haploid or diploid ONLY
double *q2p, *pdg; // pdg -> P(D|g)
double *phi, *phi_indel;
double *z, *zswap; // aux for afs
double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set
+ double **hg; // hypergeometric distribution
+ double *lf; // log factorial
double t, t1, t2;
double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
const uint8_t *PL; // point to PL
int PL_len;
};
-static void fold_array(int M, double *x)
-{
- int k;
- for (k = 0; k < M/2; ++k)
- x[k] = x[M-k] = (x[k] + x[M-k]) / 2.;
-}
-
void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
{
int i;
return 0;
}
-bcf_p1aux_t *bcf_p1_init(int n)
+bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy)
{
bcf_p1aux_t *ma;
int i;
ma = calloc(1, sizeof(bcf_p1aux_t));
ma->n1 = -1;
ma->n = n; ma->M = 2 * n;
+ if (ploidy) {
+ ma->ploidy = malloc(n);
+ memcpy(ma->ploidy, ploidy, n);
+ for (i = 0, ma->M = 0; i < n; ++i) ma->M += ploidy[i];
+ if (ma->M == 2 * n) {
+ free(ma->ploidy);
+ ma->ploidy = 0;
+ }
+ }
ma->q2p = calloc(256, sizeof(double));
ma->pdg = calloc(3 * ma->n, sizeof(double));
ma->phi = calloc(ma->M + 1, sizeof(double));
ma->phi_indel = calloc(ma->M + 1, sizeof(double));
ma->phi1 = calloc(ma->M + 1, sizeof(double));
ma->phi2 = calloc(ma->M + 1, sizeof(double));
- ma->z = calloc(2 * ma->n + 1, sizeof(double));
- ma->zswap = calloc(2 * ma->n + 1, sizeof(double));
+ ma->z = calloc(ma->M + 1, sizeof(double));
+ ma->zswap = calloc(ma->M + 1, sizeof(double));
ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
ma->z2 = calloc(ma->M + 1, sizeof(double));
- ma->afs = calloc(2 * ma->n + 1, sizeof(double));
- ma->afs1 = calloc(2 * ma->n + 1, sizeof(double));
+ ma->afs = calloc(ma->M + 1, sizeof(double));
+ ma->afs1 = calloc(ma->M + 1, sizeof(double));
+ ma->lf = calloc(ma->M + 1, sizeof(double));
for (i = 0; i < 256; ++i)
ma->q2p[i] = pow(10., -i / 10.);
+ for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1);
bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
return ma;
}
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
{
if (n1 == 0 || n1 >= b->n) return -1;
+ if (b->M != b->n * 2) {
+ fprintf(pysamerr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__);
+ return -1;
+ }
b->n1 = n1;
return 0;
}
-void bcf_p1_set_folded(bcf_p1aux_t *p1a)
-{
- if (p1a->n1 < 0) {
- p1a->is_folded = 1;
- fold_array(p1a->M, p1a->phi);
- fold_array(p1a->M, p1a->phi_indel);
- }
-}
-
void bcf_p1_destroy(bcf_p1aux_t *ma)
{
if (ma) {
- free(ma->q2p); free(ma->pdg);
+ int k;
+ free(ma->lf);
+ if (ma->hg && ma->n1 > 0) {
+ for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]);
+ free(ma->hg);
+ }
+ free(ma->ploidy); free(ma->q2p); free(ma->pdg);
free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2);
free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
free(ma->afs); free(ma->afs1);
static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
{
- int i, j, k;
+ int i, j;
long *p, tmp;
p = alloca(b->n_alleles * sizeof(long));
memset(p, 0, sizeof(long) * b->n_alleles);
for (j = 0; j < ma->n; ++j) {
const uint8_t *pi = ma->PL + j * ma->PL_len;
double *pdg = ma->pdg + j * 3;
- pdg[0] = ma->q2p[pi[b->n_alleles]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
- for (i = k = 0; i < b->n_alleles; ++i) {
- p[i] += (int)pi[k];
- k += b->n_alleles - i;
- }
+ pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+ for (i = 0; i < b->n_alleles; ++i)
+ p[i] += (int)pi[(i+1)*(i+2)/2-1];
}
for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
for (i = 1; i < b->n_alleles; ++i) // insertion sort
if ((p[i]&0xf) == 0) break;
return i;
}
-// f0 is the reference allele frequency
-static double mc_freq_iter(double f0, const bcf_p1aux_t *ma)
-{
- double f, f3[3];
- int i;
- f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
- for (i = 0, f = 0.; i < ma->n; ++i) {
- double *pdg;
- pdg = ma->pdg + i * 3;
- f += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
- / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
- }
- f /= ma->n * 2.;
- return f;
-}
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
{
double sum, g[3];
double max, f3[3], *pdg = ma->pdg + k * 3;
- int q, i, max_i;
- f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+ int q, i, max_i, ploidy;
+ ploidy = ma->ploidy? ma->ploidy[k] : 2;
+ if (ploidy == 2) {
+ f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
+ } else {
+ f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0;
+ }
for (i = 0, sum = 0.; i < 3; ++i)
sum += (g[i] = pdg[i] * f3[i]);
for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
{
double *z[2], *tmp, *pdg;
int _j, last_min, last_max;
+ assert(beg == 0 || ma->M == ma->n*2);
z[0] = ma->z;
z[1] = ma->zswap;
pdg = ma->pdg;
z[0][0] = 1.;
last_min = last_max = 0;
ma->t = 0.;
- for (_j = beg; _j < ma->n; ++_j) {
- int k, j = _j - beg, _min = last_min, _max = last_max;
- double p[3], sum;
- pdg = ma->pdg + _j * 3;
- p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
- for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
- for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
- _max += 2;
- if (_min == 0)
- k = 0, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k];
- if (_min <= 1)
- k = 1, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k] + k*(2*j+2-k) * p[1] * z[0][k-1];
- for (k = _min < 2? 2 : _min; k <= _max; ++k)
- z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k]
- + k*(2*j+2-k) * p[1] * z[0][k-1]
- + k*(k-1)* p[2] * z[0][k-2];
- for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
- ma->t += log(sum / ((2. * j + 2) * (2. * j + 1)));
- for (k = _min; k <= _max; ++k) z[1][k] /= sum;
- if (_min >= 1) z[1][_min-1] = 0.;
- if (_min >= 2) z[1][_min-2] = 0.;
- if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
- if (_j == ma->n1 - 1) { // set pop1
- ma->t1 = ma->t;
- memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
+ if (ma->M == ma->n * 2) {
+ int M = 0;
+ for (_j = beg; _j < ma->n; ++_j) {
+ int k, j = _j - beg, _min = last_min, _max = last_max, M0;
+ double p[3], sum;
+ M0 = M; M += 2;
+ pdg = ma->pdg + _j * 3;
+ p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
+ for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+ for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+ _max += 2;
+ if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+ if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+ for (k = _min < 2? 2 : _min; k <= _max; ++k)
+ z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+ for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ ma->t += log(sum / (M * (M - 1.)));
+ for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (_min >= 1) z[1][_min-1] = 0.;
+ if (_min >= 2) z[1][_min-2] = 0.;
+ if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+ if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset
+ ma->t1 = ma->t;
+ memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
+ }
+ tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+ last_min = _min; last_max = _max;
+ }
+ //for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary?
+ //for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.;
+ } else { // this block is very similar to the block above; these two might be merged in future
+ int j, M = 0;
+ for (j = 0; j < ma->n; ++j) {
+ int k, M0, _min = last_min, _max = last_max;
+ double p[3], sum;
+ pdg = ma->pdg + j * 3;
+ for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+ for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
+ M0 = M;
+ M += ma->ploidy[j];
+ if (ma->ploidy[j] == 1) {
+ p[0] = pdg[0]; p[1] = pdg[2];
+ _max++;
+ if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k];
+ for (k = _min < 1? 1 : _min; k <= _max; ++k)
+ z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1];
+ for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ ma->t += log(sum / M);
+ for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (_min >= 1) z[1][_min-1] = 0.;
+ if (j < ma->n - 1) z[1][_max+1] = 0.;
+ } else if (ma->ploidy[j] == 2) {
+ p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2];
+ _max += 2;
+ if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
+ if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
+ for (k = _min < 2? 2 : _min; k <= _max; ++k)
+ z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
+ for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ ma->t += log(sum / (M * (M - 1.)));
+ for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (_min >= 1) z[1][_min-1] = 0.;
+ if (_min >= 2) z[1][_min-2] = 0.;
+ if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+ }
+ tmp = z[0]; z[0] = z[1]; z[1] = tmp;
+ last_min = _min; last_max = _max;
}
- tmp = z[0]; z[0] = z[1]; z[1] = tmp;
- last_min = _min; last_max = _max;
}
if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
}
static void mc_cal_y(bcf_p1aux_t *ma)
{
- if (ma->n1 > 0 && ma->n1 < ma->n) {
+ if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples
int k;
long double x;
memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
} else mc_cal_y_core(ma, 0);
}
-static void contrast(bcf_p1aux_t *ma, double pc[4]) // mc_cal_y() must be called before hand
+#define CONTRAST_TINY 1e-30
+
+extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test
+
+static inline double chi2_test(int a, int b, int c, int d)
+{
+ double x, z;
+ x = (double)(a+b) * (c+d) * (b+d) * (a+c);
+ if (x == 0.) return 1;
+ z = a * d - b * c;
+ return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x);
+}
+
+// chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)]
+static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3])
+{
+ double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2];
+ int n1 = p1->n1, n2 = p1->n - p1->n1;
+ if (p < CONTRAST_TINY) return -1;
+ if (.5*k1/n1 < .5*k2/n2) x[1] += p;
+ else if (.5*k1/n1 > .5*k2/n2) x[2] += p;
+ else x[0] += p;
+ return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2);
+}
+
+static double contrast2(bcf_p1aux_t *p1, double ret[3])
{
- int k, n1 = ma->n1, n2 = ma->n - ma->n1;
- long double sum1, sum2;
- pc[0] = pc[1] = pc[2] = pc[3] = -1.;
- if (n1 <= 0 || n2 <= 0) return;
- for (k = 0, sum1 = 0.; k <= 2*n1; ++k) sum1 += ma->phi1[k] * ma->z1[k];
- for (k = 0, sum2 = 0.; k <= 2*n2; ++k) sum2 += ma->phi2[k] * ma->z2[k];
- pc[2] = ma->phi1[2*n1] * ma->z1[2*n1] / sum1;
- pc[3] = ma->phi2[2*n2] * ma->z2[2*n2] / sum2;
- for (k = 2; k < 4; ++k) {
- pc[k] = pc[k] > .5? -(-4.343 * log(1. - pc[k] + TINY) + .499) : -4.343 * log(pc[k] + TINY) + .499;
- pc[k] = (int)pc[k];
- if (pc[k] > 99) pc[k] = 99;
- if (pc[k] < -99) pc[k] = -99;
+ int k, k1, k2, k10, k20, n1, n2;
+ double sum;
+ // get n1 and n2
+ n1 = p1->n1; n2 = p1->n - p1->n1;
+ if (n1 <= 0 || n2 <= 0) return 0.;
+ if (p1->hg == 0) { // initialize the hypergeometric distribution
+ /* NB: the hg matrix may take a lot of memory when there are many samples. There is a way
+ to avoid precomputing this matrix, but it is slower and quite intricate. The following
+ computation in this block can be accelerated with a similar strategy, but perhaps this
+ is not a serious concern for now. */
+ double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1));
+ p1->hg = calloc(2*n1+1, sizeof(void*));
+ for (k1 = 0; k1 <= 2*n1; ++k1) {
+ p1->hg[k1] = calloc(2*n2+1, sizeof(double));
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp));
+ }
+ }
+ { // compute
+ long double suml = 0;
+ for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k];
+ sum = suml;
+ }
+ { // get the max k1 and k2
+ double max;
+ int max_k;
+ for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) {
+ double x = p1->phi1[k] * p1->z1[k];
+ if (x > max) max = x, max_k = k;
+ }
+ k10 = max_k;
+ for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) {
+ double x = p1->phi2[k] * p1->z2[k];
+ if (x > max) max = x, max_k = k;
+ }
+ k20 = max_k;
+ }
+ { // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N.
+ double x[3], y;
+ long double z = 0., L[2];
+ x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0;
+ for (k1 = k10; k1 >= 0; --k1) {
+ for (k2 = k20; k2 >= 0; --k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ }
+ ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2];
+ x[0] = x[1] = x[2] = 0;
+ for (k1 = k10 + 1; k1 <= 2*n1; ++k1) {
+ for (k2 = k20; k2 >= 0; --k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
+ if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
+ else z += y;
+ }
+ }
+ ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2];
+ if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened
+ ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0;
+ for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y;
+ if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why...
+ z = 1.0, ret[0] = ret[1] = ret[2] = 1./3;
+ }
+ return (double)z;
}
- pc[0] = ma->phi2[2*n2] * ma->z2[2*n2] / sum2 * (1. - ma->phi1[2*n1] * ma->z1[2*n1] / sum1);
- pc[1] = ma->phi1[2*n1] * ma->z1[2*n1] / sum1 * (1. - ma->phi2[2*n2] * ma->z2[2*n2] / sum2);
- pc[0] = pc[0] == 1.? 99 : (int)(-4.343 * log(1. - pc[0]) + .499);
- pc[1] = pc[1] == 1.? 99 : (int)(-4.343 * log(1. - pc[1]) + .499);
}
-static double mc_cal_afs(bcf_p1aux_t *ma)
+static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
{
int k;
- long double sum = 0.;
+ long double sum = 0., sum2;
double *phi = ma->is_indel? ma->phi_indel : ma->phi;
memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
mc_cal_y(ma);
+ // compute AFS
for (k = 0, sum = 0.; k <= ma->M; ++k)
sum += (long double)phi[k] * ma->z[k];
for (k = 0; k <= ma->M; ++k) {
ma->afs1[k] = phi[k] * ma->z[k] / sum;
if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
}
+ // compute folded variant probability
+ for (k = 0, sum = 0.; k <= ma->M; ++k)
+ sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+ for (k = 1, sum2 = 0.; k < ma->M; ++k)
+ sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
+ *p_var_folded = sum2 / sum;
+ *p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
+ // the expected frequency
for (k = 0, sum = 0.; k <= ma->M; ++k) {
ma->afs[k] += ma->afs1[k];
sum += k * ma->afs1[k];
return sum / ma->M;
}
-long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
-{
- long double pd = 0., g2[3];
- int i, k;
- memset(g2, 0, sizeof(long double) * 3);
- for (k = 0; k < p1a->M; ++k) {
- double f = (double)k / p1a->M, f3[3], g1[3];
- long double z = 1.;
- g1[0] = g1[1] = g1[2] = 0.;
- f3[0] = (1. - f) * (1. - f); f3[1] = 2. * f * (1. - f); f3[2] = f * f;
- for (i = 0; i < p1a->n; ++i) {
- double *pdg = p1a->pdg + i * 3;
- double x = pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
- z *= x;
- g1[0] += pdg[0] * f3[0] / x;
- g1[1] += pdg[1] * f3[1] / x;
- g1[2] += pdg[2] * f3[2] / x;
- }
- pd += p1a->phi[k] * z;
- for (i = 0; i < 3; ++i)
- g2[i] += p1a->phi[k] * z * g1[i];
- }
- for (i = 0; i < 3; ++i) g[i] = g2[i] / pd;
- return pd;
-}
-
-int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
+int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
{
int i, k;
long double sum = 0.;
ma->is_indel = bcf_is_indel(b);
+ rst->perm_rank = -1;
// set PL and PL_len
for (i = 0; i < b->n_gi; ++i) {
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
break;
}
}
+ if (i == b->n_gi) return -1; // no PL
if (b->n_alleles < 2) return -1; // FIXME: find a better solution
//
rst->rank0 = cal_pdg(b, ma);
- rst->f_exp = mc_cal_afs(ma);
- rst->p_ref = ma->is_folded? ma->afs1[ma->M] + ma->afs1[0] : ma->afs1[ma->M];
+ rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded);
+ rst->p_ref = ma->afs1[ma->M];
+ for (k = 0, sum = 0.; k < ma->M; ++k)
+ sum += ma->afs1[k];
+ rst->p_var = (double)sum;
// calculate f_flat and f_em
for (k = 0, sum = 0.; k <= ma->M; ++k)
sum += (long double)ma->z[k];
rst->f_flat += k * p;
}
rst->f_flat /= ma->M;
- { // calculate f_em
- double flast = rst->f_flat;
- for (i = 0; i < MC_MAX_EM_ITER; ++i) {
- rst->f_em = mc_freq_iter(flast, ma);
- if (fabs(rst->f_em - flast) < MC_EM_EPS) break;
- flast = rst->f_em;
- }
- }
{ // estimate equal-tail credible interval (95% level)
int l, h;
double p;
h = i;
rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
}
- rst->g[0] = rst->g[1] = rst->g[2] = -1.;
- contrast(ma, rst->pc);
+ rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
+ if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant
+ rst->p_chi2 = contrast2(ma, rst->cmp);
return 0;
}
void bcf_p1_dump_afs(bcf_p1aux_t *ma)
{
int k;
- if (ma->is_folded) fold_array(ma->M, ma->afs);
fprintf(pysamerr, "[afs]");
for (k = 0; k <= ma->M; ++k)
fprintf(pysamerr, " %d:%.3lf", k, ma->afs[ma->M - k]);
typedef struct __bcf_p1aux_t bcf_p1aux_t;
typedef struct {
- int rank0;
- double f_em, f_exp, f_flat, p_ref;
+ int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+ double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
double cil, cih;
- double pc[4];
- double g[3];
+ double cmp[3], p_chi2; // used by contrast2()
} bcf_p1rst_t;
#define MC_PTYPE_FULL 1
extern "C" {
#endif
- bcf_p1aux_t *bcf_p1_init(int n);
+ bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy);
void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_destroy(bcf_p1aux_t *ma);
- int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+ int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
void bcf_p1_dump_afs(bcf_p1aux_t *ma);
int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
- long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3]);
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
+ int bcf_em1(const bcf1_t *b, int n1, int flag, double x[9]);
+
#ifdef __cplusplus
}
#endif
return bp;
}
+int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn)
+{
+ vcf_t *v;
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s, rn;
+ int dret;
+ if (bp == 0) return -1;
+ if (!bp->is_vcf) return 0;
+ s.l = s.m = 0; s.s = 0;
+ rn.m = rn.l = h->l_nm; rn.s = h->name;
+ v = (vcf_t*)bp->v;
+ fp = gzopen(fn, "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ bcf_str2id_add(v->refhash, strdup(s.s));
+ kputs(s.s, &rn); kputc('\0', &rn);
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ h->l_nm = rn.l; h->name = rn.s;
+ bcf_hdr_sync(h);
+ free(s.s);
+ return 0;
+}
+
int vcf_close(bcf_t *bp)
{
vcf_t *v;
}
if (v->fpout) fclose(v->fpout);
free(v->line.s);
- bcf_str2id_destroy(v->refhash);
+ bcf_str2id_thorough_destroy(v->refhash);
free(v);
free(bp);
return 0;
int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
{
vcf_t *v = (vcf_t*)bp->v;
- int i, has_ref = 0, has_ver = 0;
+ int i, has_ver = 0;
if (!bp->is_vcf) return bcf_hdr_write(bp, h);
if (h->l_txt > 0) {
if (strstr(h->txt, "##fileformat=")) has_ver = 1;
- if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+ if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
- if (strstr(h->txt, "##SQ=")) has_ref = 1;
}
- if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+ if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for (i = 0; i < h->n_smpl; ++i)
fprintf(v->fpout, "\t%s", h->sns[i]);
if (k == 0) { // ref
int tid = bcf_str2id(v->refhash, p);
if (tid < 0) {
- tid = bcf_str2id_add(v->refhash, p);
+ tid = bcf_str2id_add(v->refhash, strdup(p));
kputs(p, &rn); kputc('\0', &rn);
sync = 1;
}
for (i = 0; i < b->n_gi; ++i) {
if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
- } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = 0;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ ((int32_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
((uint16_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
- } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
double _x = strtod(q, &q);
int x = (int)(_x + .499);
if (x > 255) x = 255;
((uint8_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ int x = strtol(q, &q, 10);
+ if (x > 0xffff) x = 0xffff;
+ ((uint32_t*)b->gi[i].data)[k-9] = x;
} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
y = b->n_alleles * (b->n_alleles + 1) / 2;
for (j = 0; j < y; ++j) {
x = strtod(q, &q);
- data[(k-9) * y + j] = x;
+ data[(k-9) * y + j] = x > 0? -x/10. : x;
++q;
}
}
--- /dev/null
+#include "pysam.h"
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+
+#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);
+}
fp->error = message;
}
+int bgzf_check_bgzf(const char *fn)
+{
+ BGZF *fp;
+ uint8_t buf[10],magic[10]="\037\213\010\4\0\0\0\0\0\377";
+ int n;
+
+ if ((fp = bgzf_open(fn, "r")) == 0)
+ {
+ fprintf(pysamerr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
+ return -1;
+ }
+
+#ifdef _USE_KNETFILE
+ n = knet_read(fp->x.fpr, buf, 10);
+#else
+ n = fread(buf, 1, 10, fp->file);
+#endif
+ bgzf_close(fp);
+
+ if ( n!=10 )
+ return -1;
+
+ if ( !memcmp(magic, buf, 10) ) return 1;
+ return 0;
+}
+
static BGZF *bgzf_read_init()
{
BGZF *fp;
static
BGZF*
-open_write(int fd, bool is_uncompressed)
+open_write(int fd, int compress_level) // compress_level==-1 for the default level
{
FILE* file = fdopen(fd, "w");
BGZF* fp;
fp = malloc(sizeof(BGZF));
fp->file_descriptor = fd;
fp->open_mode = 'w';
- fp->owned_file = 0; fp->is_uncompressed = is_uncompressed;
+ fp->owned_file = 0;
+ 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;
#ifdef _USE_KNETFILE
fp->x.fpw = file;
#else
fp = open_read(fd);
#endif
} else if (strchr(mode, 'w') || strchr(mode, 'W')) {
- int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
+ int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
#ifdef _WIN32
oflag |= O_BINARY;
#endif
fd = open(path, oflag, 0666);
if (fd == -1) return 0;
- fp = open_write(fd, strchr(mode, 'u')? 1 : 0);
+ { // set compress_level
+ int i;
+ 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;
+ }
+ fp = open_write(fd, compress_level);
}
if (fp != NULL) fp->owned_file = 1;
return fp;
if (mode[0] == 'r' || mode[0] == 'R') {
return open_read(fd);
} else if (mode[0] == 'w' || mode[0] == 'W') {
- return open_write(fd, strstr(mode, "u")? 1 : 0);
+ 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 open_write(fd, compress_level);
} else {
return NULL;
}
int input_length = block_length;
int compressed_length = 0;
while (1) {
- int compress_level = fp->is_uncompressed? 0 : Z_DEFAULT_COMPRESSION;
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
- int status = deflateInit2(&zs, compress_level, Z_DEFLATED,
+ int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED,
GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
if (status != Z_OK) {
report_error(fp, "deflate init failed");
// Inflate the block in fp->compressed_block into fp->uncompressed_block
z_stream zs;
+ int status;
zs.zalloc = NULL;
zs.zfree = NULL;
zs.next_in = fp->compressed_block + 18;
zs.next_out = fp->uncompressed_block;
zs.avail_out = fp->uncompressed_block_size;
- int status = inflateInit2(&zs, GZIP_WINDOW_BITS);
+ status = inflateInit2(&zs, GZIP_WINDOW_BITS);
if (status != Z_OK) {
report_error(fp, "inflate init failed");
return -1;
bgzf_read_block(BGZF* fp)
{
bgzf_byte_t header[BLOCK_HEADER_LENGTH];
- int count, size = 0;
+ int count, size = 0, block_length, remaining;
#ifdef _USE_KNETFILE
int64_t block_address = knet_tell(fp->x.fpr);
if (load_block_from_cache(fp, block_address)) return 0;
report_error(fp, "invalid block header");
return -1;
}
- int block_length = unpackInt16((uint8_t*)&header[16]) + 1;
+ block_length = unpackInt16((uint8_t*)&header[16]) + 1;
bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
- int remaining = block_length - BLOCK_HEADER_LENGTH;
+ remaining = block_length - BLOCK_HEADER_LENGTH;
#ifdef _USE_KNETFILE
count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
#else
int bytes_read = 0;
bgzf_byte_t* output = data;
while (bytes_read < length) {
- int available = fp->block_length - fp->block_offset;
+ int copy_length, available = fp->block_length - fp->block_offset;
+ bgzf_byte_t *buffer;
if (available <= 0) {
if (bgzf_read_block(fp) != 0) {
return -1;
break;
}
}
- int copy_length = bgzf_min(length-bytes_read, available);
- bgzf_byte_t* buffer = fp->uncompressed_block;
+ copy_length = bgzf_min(length-bytes_read, available);
+ buffer = fp->uncompressed_block;
memcpy(output, buffer + fp->block_offset, copy_length);
fp->block_offset += copy_length;
output += copy_length;
int bgzf_write(BGZF* fp, const void* data, int length)
{
+ const bgzf_byte_t *input = data;
+ int block_length, bytes_written;
if (fp->open_mode != 'w') {
report_error(fp, "file not open for writing");
return -1;
if (fp->uncompressed_block == NULL)
fp->uncompressed_block = malloc(fp->uncompressed_block_size);
- const bgzf_byte_t* input = data;
- int block_length = fp->uncompressed_block_size;
- int bytes_written = 0;
+ input = data;
+ block_length = fp->uncompressed_block_size;
+ bytes_written = 0;
while (bytes_written < length) {
int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
bgzf_byte_t* buffer = fp->uncompressed_block;
#include <stdint.h>
#include <stdio.h>
-#include <stdbool.h>
#include <zlib.h>
#ifdef _USE_KNETFILE
#include "knetfile.h"
typedef struct {
int file_descriptor;
char open_mode; // 'r' or 'w'
- bool owned_file, is_uncompressed;
+ int16_t owned_file, compress_level;
#ifdef _USE_KNETFILE
union {
knetFile *fpr;
int bgzf_read_block(BGZF* fp);
int bgzf_flush(BGZF* fp);
int bgzf_flush_try(BGZF *fp, int size);
+int bgzf_check_bgzf(const char *fn);
#ifdef __cplusplus
}
--- /dev/null
+#include "pysam.h"
+
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include "bam.h"
+#include "errmod.h"
+#include "faidx.h"
+
+#define ERR_DEP 0.83f
+
+typedef struct {
+ int e[2][3], p[2][2];
+} score_param_t;
+
+/* Note that although the two matrics have 10 parameters in total, only 4
+ * (probably 3) are free. Changing the scoring matrices in a sort of symmetric
+ * way will not change the result. */
+static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };
+
+typedef struct {
+ int min_baseQ, tid, max_bases;
+ uint16_t *bases;
+ bamFile fp;
+ bam_header_t *h;
+ char *ref;
+ faidx_t *fai;
+ errmod_t *em;
+} ct_t;
+
+static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
+{
+ int i, j, ret, tmp, k, sum[4], qual;
+ float q[16];
+ if (n > g->max_bases) { // enlarge g->bases
+ g->max_bases = n;
+ kroundup32(g->max_bases);
+ g->bases = realloc(g->bases, g->max_bases * 2);
+ }
+ for (i = k = 0; i < n; ++i) {
+ const bam_pileup1_t *p = plp + i;
+ uint8_t *seq;
+ int q, baseQ, b;
+ if (p->is_refskip || p->is_del) continue;
+ baseQ = bam1_qual(p->b)[p->qpos];
+ if (baseQ < g->min_baseQ) continue;
+ seq = bam1_seq(p->b);
+ b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
+ if (b > 3) continue;
+ q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+ if (q < 4) q = 4;
+ if (q > 63) q = 63;
+ g->bases[k++] = q<<5 | bam1_strand(p->b)<<4 | b;
+ }
+ if (k == 0) return 0;
+ errmod_cal(g->em, k, 4, g->bases, q);
+ for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
+ for (i = 1; i < 4; ++i) // insertion sort
+ for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
+ tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
+ qual = (sum[1]>>2) - (sum[0]>>2);
+ k = k < 256? k : 255;
+ ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
+ return ret<<8|k;
+}
+
+static void process_cns(bam_header_t *h, int tid, int l, uint16_t *cns)
+{
+ int i, f[2][2], *prev, *curr, *swap_tmp, s;
+ uint8_t *b; // backtrack array
+ b = calloc(l, 1);
+ f[0][0] = f[0][1] = 0;
+ prev = f[0]; curr = f[1];
+ // fill the backtrack matrix
+ for (i = 0; i < l; ++i) {
+ int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
+ int tmp0, tmp1;
+ // compute f[0]
+ tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
+ tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
+ if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
+ else curr[0] = tmp1, b[i] = 1;
+ // compute f[1]
+ tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
+ tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
+ if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
+ else curr[1] = tmp1, b[i] |= 1<<1;
+ // swap
+ swap_tmp = prev; prev = curr; curr = swap_tmp;
+ }
+ // backtrack
+ s = prev[0] > prev[1]? 0 : 1;
+ for (i = l - 1; i > 0; --i) {
+ b[i] |= s<<2;
+ s = b[i]>>s&1;
+ }
+ // print
+ for (i = 0, s = -1; i <= l; ++i) {
+ if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
+ if (s >= 0) {
+ int j;
+ printf("%s:%d-%d\t0\t%s\t%d\t60\t%dM\t*\t0\t0\t", h->target_name[tid], s+1, i, h->target_name[tid], s+1, i-s);
+ for (j = s; j < i; ++j) {
+ int c = cns[j]>>8;
+ if (c == 0) putchar('N');
+ else putchar("ACGT"[c&3]);
+ }
+ putchar('\t');
+ for (j = s; j < i; ++j)
+ putchar(33 + (cns[j]>>8>>2));
+ putchar('\n');
+ }
+ //if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
+ s = -1;
+ } else if ((b[i]>>2&3) && s < 0) s = i;
+ }
+ free(b);
+}
+
+static int read_aln(void *data, bam1_t *b)
+{
+ extern int bam_prob_realn_core(bam1_t *b, const char *ref, int flag);
+ ct_t *g = (ct_t*)data;
+ int ret, len;
+ ret = bam_read1(g->fp, b);
+ if (ret >= 0 && g->fai && b->core.tid >= 0 && (b->core.flag&4) == 0) {
+ if (b->core.tid != g->tid) { // then load the sequence
+ free(g->ref);
+ g->ref = fai_fetch(g->fai, g->h->target_name[b->core.tid], &len);
+ g->tid = b->core.tid;
+ }
+ bam_prob_realn_core(b, g->ref, 1<<1|1);
+ }
+ return ret;
+}
+
+int main_cut_target(int argc, char *argv[])
+{
+ int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
+ const bam_pileup1_t *p;
+ bam_plp_t plp;
+ uint16_t *cns;
+ ct_t g;
+
+ memset(&g, 0, sizeof(ct_t));
+ g.min_baseQ = 13; g.tid = -1;
+ while ((c = getopt(argc, argv, "f:Q:i:o:0:1:2:")) >= 0) {
+ switch (c) {
+ case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
+ case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
+ case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
+ case '1': g_param.e[1][1] = atoi(optarg); break;
+ case '2': g_param.e[1][2] = atoi(optarg); break;
+ case 'f': g.fai = fai_load(optarg);
+ if (g.fai == 0) fprintf(pysamerr, "[%s] fail to load the fasta index.\n", __func__);
+ break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(pysamerr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>\n");
+ return 1;
+ }
+ l = max_l = 0; cns = 0;
+ g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+ g.h = bam_header_read(g.fp);
+ g.em = errmod_init(1 - ERR_DEP);
+ plp = bam_plp_init(read_aln, &g);
+ while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
+ if (tid < 0) break;
+ if (tid != lasttid) { // change of chromosome
+ if (cns) process_cns(g.h, lasttid, l, cns);
+ if (max_l < g.h->target_len[tid]) {
+ max_l = g.h->target_len[tid];
+ kroundup32(max_l);
+ cns = realloc(cns, max_l * 2);
+ }
+ l = g.h->target_len[tid];
+ memset(cns, 0, max_l * 2);
+ lasttid = tid;
+ }
+ cns[pos] = gencns(&g, n, p);
+ lastpos = pos;
+ }
+ process_cns(g.h, lasttid, l, cns);
+ free(cns);
+ bam_header_destroy(g.h);
+ bam_plp_destroy(plp);
+ bam_close(g.fp);
+ if (g.fai) {
+ fai_destroy(g.fai); free(g.ref);
+ }
+ errmod_destroy(g.em);
+ free(g.bases);
+ return 0;
+}
errmod_t *errmod_init(float depcorr);
void errmod_destroy(errmod_t *em);
+
+/*
+ n: number of bases
+ m: maximum base
+ bases[i]: qual:6, strand:1, base:4
+ q[i*m+j]: phred-scaled likelihood of (i,j)
+ */
int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);
#endif
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
+#include <stdint.h>
#include "faidx.h"
#include "khash.h"
/* The MIT License
- Copyright (c) 2008 Genome Research Ltd (GRL).
+ Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
SOFTWARE.
*/
-/* Contact: Heng Li <lh3@sanger.ac.uk> */
-
/*
An example:
*/
/*
+ 2011-02-14 (0.2.5):
+
+ * Allow to declare global functions.
+
+ 2009-09-26 (0.2.4):
+
+ * Improve portability
+
2008-09-19 (0.2.3):
* Corrected the example
@copyright Heng Li
*/
-#define AC_VERSION_KHASH_H "0.2.2"
+#define AC_VERSION_KHASH_H "0.2.5"
-#include <stdint.h>
#include <stdlib.h>
#include <string.h>
+#include <limits.h>
+
+/* compipler specific configuration */
+
+#if UINT_MAX == 0xffffffffu
+typedef unsigned int khint32_t;
+#elif ULONG_MAX == 0xffffffffu
+typedef unsigned long khint32_t;
+#endif
+
+#if ULONG_MAX == ULLONG_MAX
+typedef unsigned long khint64_t;
+#else
+typedef unsigned long long khint64_t;
+#endif
+
+#ifdef _MSC_VER
+#define inline __inline
+#endif
-typedef uint32_t khint_t;
+typedef khint32_t khint_t;
typedef khint_t khiter_t;
#define __ac_HASH_PRIME_SIZE 32
-static const uint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
+static const khint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
{
0ul, 3ul, 11ul, 23ul, 53ul,
97ul, 193ul, 389ul, 769ul, 1543ul,
static const double __ac_HASH_UPPER = 0.77;
-#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+#define KHASH_DECLARE(name, khkey_t, khval_t) \
+ typedef struct { \
+ khint_t n_buckets, size, n_occupied, upper_bound; \
+ khint32_t *flags; \
+ khkey_t *keys; \
+ khval_t *vals; \
+ } kh_##name##_t; \
+ extern kh_##name##_t *kh_init_##name(); \
+ extern void kh_destroy_##name(kh_##name##_t *h); \
+ extern void kh_clear_##name(kh_##name##_t *h); \
+ extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \
+ extern void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
+ extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
+ extern void kh_del_##name(kh_##name##_t *h, khint_t x);
+
+#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
typedef struct { \
khint_t n_buckets, size, n_occupied, upper_bound; \
- uint32_t *flags; \
+ khint32_t *flags; \
khkey_t *keys; \
khval_t *vals; \
} kh_##name##_t; \
- static inline kh_##name##_t *kh_init_##name() { \
+ SCOPE kh_##name##_t *kh_init_##name() { \
return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \
} \
- static inline void kh_destroy_##name(kh_##name##_t *h) \
+ SCOPE void kh_destroy_##name(kh_##name##_t *h) \
{ \
if (h) { \
free(h->keys); free(h->flags); \
free(h); \
} \
} \
- static inline void kh_clear_##name(kh_##name##_t *h) \
+ SCOPE void kh_clear_##name(kh_##name##_t *h) \
{ \
if (h && h->flags) { \
- memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(uint32_t)); \
+ memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(khint32_t)); \
h->size = h->n_occupied = 0; \
} \
} \
- static inline khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
+ SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
{ \
if (h->n_buckets) { \
khint_t inc, k, i, last; \
return __ac_iseither(h->flags, i)? h->n_buckets : i; \
} else return 0; \
} \
- static inline void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
+ SCOPE void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
{ \
- uint32_t *new_flags = 0; \
+ khint32_t *new_flags = 0; \
khint_t j = 1; \
{ \
khint_t t = __ac_HASH_PRIME_SIZE - 1; \
new_n_buckets = __ac_prime_list[t+1]; \
if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; \
else { \
- new_flags = (uint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(uint32_t)); \
- memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(uint32_t)); \
+ new_flags = (khint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
+ memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
if (h->n_buckets < new_n_buckets) { \
h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
if (kh_is_map) \
h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
} \
} \
- static inline khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
+ SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
{ \
khint_t x; \
if (h->n_occupied >= h->upper_bound) { \
} else *ret = 0; \
return x; \
} \
- static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \
+ SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
{ \
if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \
__ac_set_isdel_true(h->flags, x); \
} \
}
+#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+ KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
+
/* --- BEGIN OF HASH FUNCTIONS --- */
/*! @function
@abstract Integer hash function
- @param key The integer [uint32_t]
+ @param key The integer [khint32_t]
@return The hash value [khint_t]
*/
-#define kh_int_hash_func(key) (uint32_t)(key)
+#define kh_int_hash_func(key) (khint32_t)(key)
/*! @function
@abstract Integer comparison function
*/
#define kh_int_hash_equal(a, b) ((a) == (b))
/*! @function
@abstract 64-bit integer hash function
- @param key The integer [uint64_t]
+ @param key The integer [khint64_t]
@return The hash value [khint_t]
*/
-#define kh_int64_hash_func(key) (uint32_t)((key)>>33^(key)^(key)<<11)
+#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
/*! @function
@abstract 64-bit integer comparison function
*/
@param name Name of the hash table [symbol]
*/
#define KHASH_SET_INIT_INT(name) \
- KHASH_INIT(name, uint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
+ KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
/*! @function
@abstract Instantiate a hash map containing integer keys
@param khval_t Type of values [type]
*/
#define KHASH_MAP_INIT_INT(name, khval_t) \
- KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
+ KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
/*! @function
@abstract Instantiate a hash map containing 64-bit integer keys
@param name Name of the hash table [symbol]
*/
#define KHASH_SET_INIT_INT64(name) \
- KHASH_INIT(name, uint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
+ KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
/*! @function
@abstract Instantiate a hash map containing 64-bit integer keys
@param khval_t Type of values [type]
*/
#define KHASH_MAP_INIT_INT64(name, khval_t) \
- KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
+ KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
typedef const char *kh_cstr_t;
/*! @function
/* The MIT License
- Copyright (c) 2008 Genome Research Ltd (GRL).
+ Copyright (c) 2008 by Genome Research Ltd (GRL).
+ 2010 by Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
SOFTWARE.
*/
-/* Contact: Heng Li <lh3@sanger.ac.uk> */
-
/* 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 */
+ Windows as well. -ac */
#include <time.h>
#include <stdio.h>
int on = 1, fd;
struct linger lng = { 0, 0 };
- struct addrinfo hints, *res;
+ struct addrinfo hints, *res = 0;
memset(&hints, 0, sizeof(struct addrinfo));
hints.ai_family = AF_UNSPEC;
hints.ai_socktype = SOCK_STREAM;
const char *p, *start;
if (sep) { // set up the table
if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
- aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
- for (p = sep; *p; ++p)
- aux->tab[*p/64] |= 1ull<<(*p%64);
+ aux->finished = 0;
+ if (sep[1]) {
+ aux->sep = -1;
+ aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
+ for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);
+ } else aux->sep = sep[0];
+ }
+ if (aux->finished) return 0;
+ else if (str) aux->p = str - 1, aux->finished = 0;
+ if (aux->sep < 0) {
+ for (p = start = aux->p + 1; *p; ++p)
+ if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
+ } else {
+ for (p = start = aux->p + 1; *p; ++p)
+ if (*p == aux->sep) break;
}
- if (str) aux->p = str - 1, aux->tab[0] &= ~1ull;
- else if (aux->tab[0]&1) return 0;
- for (p = start = aux->p + 1; *p; ++p)
- if (aux->tab[*p/64]>>(*p%64)&1) break;
aux->p = p; // end of token
- if (*p == 0) aux->tab[0] |= 1; // no more tokens
+ if (*p == 0) aux->finished = 1; // no more tokens
return (char*)start;
}
typedef struct {
uint64_t tab[4];
+ int sep, finished;
const char *p; // end of the current token
} ks_tokaux_t;
--- /dev/null
+#include "pysam.h"
+
+/*
+ * This code implements the MD5 message-digest algorithm.
+ * The algorithm is due to Ron Rivest. This code was
+ * written by Colin Plumb in 1993, no copyright is claimed.
+ * This code is in the public domain; do with it what you wish.
+ *
+ * Equivalent code is available from RSA Data Security, Inc.
+ * This code has been tested against that, and is equivalent,
+ * except that you don't need to include two pages of legalese
+ * with every copy.
+ *
+ * To compute the message digest of a chunk of bytes, declare an
+ * MD5Context structure, pass it to MD5Init, call MD5Update as
+ * needed on buffers full of bytes, and then call MD5Final, which
+ * will fill a supplied 16-byte array with the digest.
+ */
+
+/* Brutally hacked by John Walker back from ANSI C to K&R (no
+ prototypes) to maintain the tradition that Netfone will compile
+ with Sun's original "cc". */
+
+#include <string.h>
+#include "md5.h"
+
+#ifndef HIGHFIRST
+#define byteReverse(buf, len) /* Nothing */
+#else
+/*
+ * Note: this code is harmless on little-endian machines.
+ */
+void byteReverse(buf, longs)
+ unsigned char *buf; unsigned longs;
+{
+ uint32_t t;
+ do {
+ t = (uint32_t) ((unsigned) buf[3] << 8 | buf[2]) << 16 |
+ ((unsigned) buf[1] << 8 | buf[0]);
+ *(uint32_t *) buf = t;
+ buf += 4;
+ } while (--longs);
+}
+#endif
+
+void MD5Transform(uint32_t buf[4], uint32_t in[16]);
+
+
+/*
+ * Start MD5 accumulation. Set bit count to 0 and buffer to mysterious
+ * initialization constants.
+ */
+void MD5Init(ctx)
+ struct MD5Context *ctx;
+{
+ ctx->buf[0] = 0x67452301;
+ ctx->buf[1] = 0xefcdab89;
+ ctx->buf[2] = 0x98badcfe;
+ ctx->buf[3] = 0x10325476;
+
+ ctx->bits[0] = 0;
+ ctx->bits[1] = 0;
+}
+
+/*
+ * Update context to reflect the concatenation of another buffer full
+ * of bytes.
+ */
+void MD5Update(ctx, buf, len)
+ struct MD5Context *ctx; unsigned char *buf; unsigned len;
+{
+ uint32_t t;
+
+ /* Update bitcount */
+
+ t = ctx->bits[0];
+ if ((ctx->bits[0] = t + ((uint32_t) len << 3)) < t)
+ ctx->bits[1]++; /* Carry from low to high */
+ ctx->bits[1] += len >> 29;
+
+ t = (t >> 3) & 0x3f; /* Bytes already in shsInfo->data */
+
+ /* Handle any leading odd-sized chunks */
+
+ if (t) {
+ unsigned char *p = (unsigned char *) ctx->in + t;
+
+ t = 64 - t;
+ if (len < t) {
+ memcpy(p, buf, len);
+ return;
+ }
+ memcpy(p, buf, t);
+ byteReverse(ctx->in, 16);
+ MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+ buf += t;
+ len -= t;
+ }
+ /* Process data in 64-byte chunks */
+
+ while (len >= 64) {
+ memcpy(ctx->in, buf, 64);
+ byteReverse(ctx->in, 16);
+ MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+ buf += 64;
+ len -= 64;
+ }
+
+ /* Handle any remaining bytes of data. */
+
+ memcpy(ctx->in, buf, len);
+}
+
+/*
+ * Final wrapup - pad to 64-byte boundary with the bit pattern
+ * 1 0* (64-bit count of bits processed, MSB-first)
+ */
+void MD5Final(digest, ctx)
+ unsigned char digest[16]; struct MD5Context *ctx;
+{
+ unsigned count;
+ unsigned char *p;
+
+ /* Compute number of bytes mod 64 */
+ count = (ctx->bits[0] >> 3) & 0x3F;
+
+ /* Set the first char of padding to 0x80. This is safe since there is
+ always at least one byte free */
+ p = ctx->in + count;
+ *p++ = 0x80;
+
+ /* Bytes of padding needed to make 64 bytes */
+ count = 64 - 1 - count;
+
+ /* Pad out to 56 mod 64 */
+ if (count < 8) {
+ /* Two lots of padding: Pad the first block to 64 bytes */
+ memset(p, 0, count);
+ byteReverse(ctx->in, 16);
+ MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+
+ /* Now fill the next block with 56 bytes */
+ memset(ctx->in, 0, 56);
+ } else {
+ /* Pad block to 56 bytes */
+ memset(p, 0, count - 8);
+ }
+ byteReverse(ctx->in, 14);
+
+ /* Append length in bits and transform */
+ ((uint32_t *) ctx->in)[14] = ctx->bits[0];
+ ((uint32_t *) ctx->in)[15] = ctx->bits[1];
+
+ MD5Transform(ctx->buf, (uint32_t *) ctx->in);
+ byteReverse((unsigned char *) ctx->buf, 4);
+ memcpy(digest, ctx->buf, 16);
+ memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
+}
+
+
+/* The four core functions - F1 is optimized somewhat */
+
+/* #define F1(x, y, z) (x & y | ~x & z) */
+#define F1(x, y, z) (z ^ (x & (y ^ z)))
+#define F2(x, y, z) F1(z, x, y)
+#define F3(x, y, z) (x ^ y ^ z)
+#define F4(x, y, z) (y ^ (x | ~z))
+
+/* This is the central step in the MD5 algorithm. */
+#define MD5STEP(f, w, x, y, z, data, s) \
+ ( w += f(x, y, z) + data, w = w<<s | w>>(32-s), w += x )
+
+/*
+ * The core of the MD5 algorithm, this alters an existing MD5 hash to
+ * reflect the addition of 16 longwords of new data. MD5Update blocks
+ * the data and converts bytes into longwords for this routine.
+ */
+void MD5Transform(buf, in)
+ uint32_t buf[4]; uint32_t in[16];
+{
+ register uint32_t a, b, c, d;
+
+ a = buf[0];
+ b = buf[1];
+ c = buf[2];
+ d = buf[3];
+
+ MD5STEP(F1, a, b, c, d, in[0] + 0xd76aa478, 7);
+ MD5STEP(F1, d, a, b, c, in[1] + 0xe8c7b756, 12);
+ MD5STEP(F1, c, d, a, b, in[2] + 0x242070db, 17);
+ MD5STEP(F1, b, c, d, a, in[3] + 0xc1bdceee, 22);
+ MD5STEP(F1, a, b, c, d, in[4] + 0xf57c0faf, 7);
+ MD5STEP(F1, d, a, b, c, in[5] + 0x4787c62a, 12);
+ MD5STEP(F1, c, d, a, b, in[6] + 0xa8304613, 17);
+ MD5STEP(F1, b, c, d, a, in[7] + 0xfd469501, 22);
+ MD5STEP(F1, a, b, c, d, in[8] + 0x698098d8, 7);
+ MD5STEP(F1, d, a, b, c, in[9] + 0x8b44f7af, 12);
+ MD5STEP(F1, c, d, a, b, in[10] + 0xffff5bb1, 17);
+ MD5STEP(F1, b, c, d, a, in[11] + 0x895cd7be, 22);
+ MD5STEP(F1, a, b, c, d, in[12] + 0x6b901122, 7);
+ MD5STEP(F1, d, a, b, c, in[13] + 0xfd987193, 12);
+ MD5STEP(F1, c, d, a, b, in[14] + 0xa679438e, 17);
+ MD5STEP(F1, b, c, d, a, in[15] + 0x49b40821, 22);
+
+ MD5STEP(F2, a, b, c, d, in[1] + 0xf61e2562, 5);
+ MD5STEP(F2, d, a, b, c, in[6] + 0xc040b340, 9);
+ MD5STEP(F2, c, d, a, b, in[11] + 0x265e5a51, 14);
+ MD5STEP(F2, b, c, d, a, in[0] + 0xe9b6c7aa, 20);
+ MD5STEP(F2, a, b, c, d, in[5] + 0xd62f105d, 5);
+ MD5STEP(F2, d, a, b, c, in[10] + 0x02441453, 9);
+ MD5STEP(F2, c, d, a, b, in[15] + 0xd8a1e681, 14);
+ MD5STEP(F2, b, c, d, a, in[4] + 0xe7d3fbc8, 20);
+ MD5STEP(F2, a, b, c, d, in[9] + 0x21e1cde6, 5);
+ MD5STEP(F2, d, a, b, c, in[14] + 0xc33707d6, 9);
+ MD5STEP(F2, c, d, a, b, in[3] + 0xf4d50d87, 14);
+ MD5STEP(F2, b, c, d, a, in[8] + 0x455a14ed, 20);
+ MD5STEP(F2, a, b, c, d, in[13] + 0xa9e3e905, 5);
+ MD5STEP(F2, d, a, b, c, in[2] + 0xfcefa3f8, 9);
+ MD5STEP(F2, c, d, a, b, in[7] + 0x676f02d9, 14);
+ MD5STEP(F2, b, c, d, a, in[12] + 0x8d2a4c8a, 20);
+
+ MD5STEP(F3, a, b, c, d, in[5] + 0xfffa3942, 4);
+ MD5STEP(F3, d, a, b, c, in[8] + 0x8771f681, 11);
+ MD5STEP(F3, c, d, a, b, in[11] + 0x6d9d6122, 16);
+ MD5STEP(F3, b, c, d, a, in[14] + 0xfde5380c, 23);
+ MD5STEP(F3, a, b, c, d, in[1] + 0xa4beea44, 4);
+ MD5STEP(F3, d, a, b, c, in[4] + 0x4bdecfa9, 11);
+ MD5STEP(F3, c, d, a, b, in[7] + 0xf6bb4b60, 16);
+ MD5STEP(F3, b, c, d, a, in[10] + 0xbebfbc70, 23);
+ MD5STEP(F3, a, b, c, d, in[13] + 0x289b7ec6, 4);
+ MD5STEP(F3, d, a, b, c, in[0] + 0xeaa127fa, 11);
+ MD5STEP(F3, c, d, a, b, in[3] + 0xd4ef3085, 16);
+ MD5STEP(F3, b, c, d, a, in[6] + 0x04881d05, 23);
+ MD5STEP(F3, a, b, c, d, in[9] + 0xd9d4d039, 4);
+ MD5STEP(F3, d, a, b, c, in[12] + 0xe6db99e5, 11);
+ MD5STEP(F3, c, d, a, b, in[15] + 0x1fa27cf8, 16);
+ MD5STEP(F3, b, c, d, a, in[2] + 0xc4ac5665, 23);
+
+ MD5STEP(F4, a, b, c, d, in[0] + 0xf4292244, 6);
+ MD5STEP(F4, d, a, b, c, in[7] + 0x432aff97, 10);
+ MD5STEP(F4, c, d, a, b, in[14] + 0xab9423a7, 15);
+ MD5STEP(F4, b, c, d, a, in[5] + 0xfc93a039, 21);
+ MD5STEP(F4, a, b, c, d, in[12] + 0x655b59c3, 6);
+ MD5STEP(F4, d, a, b, c, in[3] + 0x8f0ccc92, 10);
+ MD5STEP(F4, c, d, a, b, in[10] + 0xffeff47d, 15);
+ MD5STEP(F4, b, c, d, a, in[1] + 0x85845dd1, 21);
+ MD5STEP(F4, a, b, c, d, in[8] + 0x6fa87e4f, 6);
+ MD5STEP(F4, d, a, b, c, in[15] + 0xfe2ce6e0, 10);
+ MD5STEP(F4, c, d, a, b, in[6] + 0xa3014314, 15);
+ MD5STEP(F4, b, c, d, a, in[13] + 0x4e0811a1, 21);
+ MD5STEP(F4, a, b, c, d, in[4] + 0xf7537e82, 6);
+ MD5STEP(F4, d, a, b, c, in[11] + 0xbd3af235, 10);
+ MD5STEP(F4, c, d, a, b, in[2] + 0x2ad7d2bb, 15);
+ MD5STEP(F4, b, c, d, a, in[9] + 0xeb86d391, 21);
+
+ buf[0] += a;
+ buf[1] += b;
+ buf[2] += c;
+ buf[3] += d;
+}
+
+/* lh3: the following code is added by me */
+
+#ifdef MD5SUM_MAIN
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#define HEX_STR "0123456789abcdef"
+
+static void md5_one(const char *fn)
+{
+ unsigned char buf[4096], digest[16];
+ MD5_CTX md5;
+ int l;
+ FILE *fp;
+
+ fp = strcmp(fn, "-")? fopen(fn, "r") : stdin;
+ if (fp == 0) {
+ fprintf(pysamerr, "md5sum: %s: No such file or directory\n", fn);
+ exit(1);
+ }
+ MD5Init(&md5);
+ while ((l = fread(buf, 1, 4096, fp)) > 0)
+ MD5Update(&md5, buf, l);
+ MD5Final(digest, &md5);
+ if (fp != stdin) fclose(fp);
+ for (l = 0; l < 16; ++l)
+ printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]);
+ printf(" %s\n", fn);
+}
+int main(int argc, char *argv[])
+{
+ int i;
+ if (argc == 1) md5_one("-");
+ else for (i = 1; i < argc; ++i) md5_one(argv[i]);
+ return 0;
+}
+#endif
--- /dev/null
+/*
+ This file is adapted from a program in this page:
+
+ http://www.fourmilab.ch/md5/
+
+ The original source code does not work on 64-bit machines due to the
+ wrong typedef "uint32". I also added prototypes.
+
+ -lh3
+ */
+
+#ifndef MD5_H
+#define MD5_H
+
+/* The following tests optimise behaviour on little-endian
+ machines, where there is no need to reverse the byte order
+ of 32 bit words in the MD5 computation. By default,
+ HIGHFIRST is defined, which indicates we're running on a
+ big-endian (most significant byte first) machine, on which
+ the byteReverse function in md5.c must be invoked. However,
+ byteReverse is coded in such a way that it is an identity
+ function when run on a little-endian machine, so calling it
+ on such a platform causes no harm apart from wasting time.
+ If the platform is known to be little-endian, we speed
+ things up by undefining HIGHFIRST, which defines
+ byteReverse as a null macro. Doing things in this manner
+ insures we work on new platforms regardless of their byte
+ order. */
+
+#define HIGHFIRST
+
+#if __LITTLE_ENDIAN__ != 0
+#undef HIGHFIRST
+#endif
+
+#include <stdint.h>
+
+struct MD5Context {
+ uint32_t buf[4];
+ uint32_t bits[2];
+ unsigned char in[64];
+};
+
+void MD5Init(struct MD5Context *ctx);
+void MD5Update(struct MD5Context *ctx, unsigned char *buf, unsigned len);
+void MD5Final(unsigned char digest[16], struct MD5Context *ctx);
+
+/*
+ * This is needed to make RSAREF happy on some MS-DOS compilers.
+ */
+typedef struct MD5Context MD5_CTX;
+
+/* Define CHECK_HARDWARE_PROPERTIES to have main,c verify
+ byte order and uint32_t settings. */
+#define CHECK_HARDWARE_PROPERTIES
+
+#endif /* !MD5_H */
--- /dev/null
+// Windows-specific code, include with:\r
+// #ifdef _MSC_VER\r
+// #include <msvc_compat.h>\r
+// #endif\r
+\r
+//#define _CRT_SECURE_NO_WARNINGS\r
+#ifndef MSVC_COMPAT_H\r
+#define MSVC_COMPAT_H\r
+\r
+#define inline __inline\r
+#define __func__ __FUNCTION__\r
+\r
+#include <float.h>\r
+#define isnan _isnan\r
+static int isinf(double x) {\r
+ int y = _finite(x);\r
+ if(y == 0) {\r
+ return 0;\r
+ } else {\r
+ return 1;\r
+ }\r
+}\r
+#define alloca _alloca\r
+#define atoll _atoi64\r
+\r
+#define ftello ftell\r
+
+typedef int bool;\r
+\r
+static int R_OK = 4;
+\r
+#ifndef lgamma\r
+/* Log gamma function\r
+ * \log{\Gamma(z)}\r
+ * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245\r
+ */\r
+static double lgamma(double z)\r
+{\r
+ double x = 0;\r
+ x += 0.1659470187408462e-06 / (z+7);\r
+ x += 0.9934937113930748e-05 / (z+6);\r
+ x -= 0.1385710331296526 / (z+5);\r
+ x += 12.50734324009056 / (z+4);\r
+ x -= 176.6150291498386 / (z+3);\r
+ x += 771.3234287757674 / (z+2);\r
+ x -= 1259.139216722289 / (z+1);\r
+ x += 676.5203681218835 / z;\r
+ x += 0.9999999999995183;\r
+ return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);\r
+}\r
+#endif\r
+\r
+#ifndef M_LN10\r
+#define M_LN10 2.30258509299404568402\r
+#endif\r
+#ifndef M_LN2\r
+#define M_LN2 0.69314718055994530942\r
+#endif\r
+
+#endif\r
--- /dev/null
+#include "pysam.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <math.h>
+#include <zlib.h>
+#include "bam.h"
+#include "errmod.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define MAX_VARS 256
+#define FLIP_PENALTY 2
+#define FLIP_THRES 4
+#define MASK_THRES 3
+
+#define FLAG_FIX_CHIMERA 0x1
+#define FLAG_LIST_EXCL 0x4
+#define FLAG_DROP_AMBI 0x8
+
+typedef struct {
+ // configurations, initialized in the main function
+ int flag, k, min_baseQ, min_varLOD, max_depth;
+ // other global variables
+ int vpos_shift;
+ bamFile fp;
+ char *pre;
+ bamFile out[3];
+ // alignment queue
+ int n, m;
+ bam1_t **b;
+} phaseg_t;
+
+typedef struct {
+ int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation!
+ int vpos, beg, end;
+ uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1;
+ uint32_t in:16, out:16; // in-phase and out-phase
+} frag_t, *frag_p;
+
+#define rseq_lt(a,b) ((a)->vpos < (b)->vpos)
+
+#include "khash.h"
+KHASH_SET_INIT_INT64(set64)
+KHASH_MAP_INIT_INT64(64, frag_t)
+
+typedef khash_t(64) nseq_t;
+
+#include "ksort.h"
+KSORT_INIT(rseq, frag_p, rseq_lt)
+
+static char nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+
+static inline uint64_t X31_hash_string(const char *s)
+{
+ uint64_t h = *s;
+ if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+ return h;
+}
+
+static void count1(int l, const uint8_t *seq, int *cnt)
+{
+ int i, j, n_ambi;
+ uint32_t z, x;
+ if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous
+ for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases
+ if (seq[i] == 0) ++n_ambi;
+ if (l - n_ambi <= 1) return; // only one SNP
+ for (x = 0; x < 1u<<n_ambi; ++x) { // count
+ for (i = j = 0, z = 0; i < l; ++i) {
+ int c;
+ if (seq[i]) c = seq[i] - 1;
+ else {
+ c = x>>j&1;
+ ++j;
+ }
+ z = z<<1 | c;
+ }
+ ++cnt[z];
+ }
+}
+
+static int **count_all(int l, int vpos, nseq_t *hash)
+{
+ khint_t k;
+ int i, j, **cnt;
+ uint8_t *seq;
+ seq = calloc(l, 1);
+ cnt = calloc(vpos, sizeof(void*));
+ for (i = 0; i < vpos; ++i) cnt[i] = calloc(1<<l, sizeof(int));
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos >= vpos || f->single) continue; // out of region; or singleton
+ if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right
+ f->single = 1;
+ continue;
+ }
+ for (j = 1; j < f->vlen; ++j) {
+ for (i = 0; i < l; ++i)
+ seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)];
+ count1(l, seq, cnt[f->vpos + j]);
+ }
+ }
+ }
+ free(seq);
+ return cnt;
+}
+
+// phasing
+static int8_t *dynaprog(int l, int vpos, int **w)
+{
+ int *f[2], *curr, *prev, max, i;
+ int8_t **b, *h = 0;
+ uint32_t x, z = 1u<<(l-1), mask = (1u<<l) - 1;
+ f[0] = calloc(z, sizeof(int));
+ f[1] = calloc(z, sizeof(int));
+ b = calloc(vpos, sizeof(void*));
+ prev = f[0]; curr = f[1];
+ // fill the backtrack matrix
+ for (i = 0; i < vpos; ++i) {
+ int *wi = w[i], *tmp;
+ int8_t *bi;
+ bi = b[i] = calloc(z, 1);
+ /* In the following, x is the current state, which is the
+ * lexicographically smaller local haplotype. xc is the complement of
+ * x, or the larger local haplotype; y0 and y1 are the two predecessors
+ * of x. */
+ for (x = 0; x < z; ++x) { // x0 is the smaller
+ uint32_t y0, y1, xc;
+ int c0, c1;
+ xc = ~x&mask; y0 = x>>1; y1 = xc>>1;
+ c0 = prev[y0] + wi[x] + wi[xc];
+ c1 = prev[y1] + wi[x] + wi[xc];
+ if (c0 > c1) bi[x] = 0, curr[x] = c0;
+ else bi[x] = 1, curr[x] = c1;
+ }
+ tmp = prev; prev = curr; curr = tmp; // swap
+ }
+ { // backtrack
+ uint32_t max_x = 0;
+ int which = 0;
+ h = calloc(vpos, 1);
+ for (x = 0, max = 0, max_x = 0; x < z; ++x)
+ if (prev[x] > max) max = prev[x], max_x = x;
+ for (i = vpos - 1, x = max_x; i >= 0; --i) {
+ h[i] = which? (~x&1) : (x&1);
+ which = b[i][x]? !which : which;
+ x = b[i][x]? (~x&mask)>>1 : x>>1;
+ }
+ }
+ // free
+ for (i = 0; i < vpos; ++i) free(b[i]);
+ free(f[0]); free(f[1]); free(b);
+ return h;
+}
+
+// phase each fragment
+static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip)
+{
+ khint_t k;
+ uint64_t *pcnt;
+ uint32_t *left, *rght, max;
+ left = rght = 0; max = 0;
+ pcnt = calloc(vpos, 8);
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ int i, c[2];
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos >= vpos) continue;
+ // get the phase
+ c[0] = c[1] = 0;
+ for (i = 0; i < f->vlen; ++i) {
+ if (f->seq[i] == 0) continue;
+ ++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1];
+ }
+ f->phase = c[0] > c[1]? 0 : 1;
+ f->in = c[f->phase]; f->out = c[1 - f->phase];
+ f->phased = f->in == f->out? 0 : 1;
+ f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0;
+ // fix chimera
+ f->flip = 0;
+ if (flip && c[0] >= 3 && c[1] >= 3) {
+ int sum[2], m, mi, md;
+ if (f->vlen > max) { // enlarge the array
+ max = f->vlen;
+ kroundup32(max);
+ left = realloc(left, max * 4);
+ rght = realloc(rght, max * 4);
+ }
+ for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts
+ if (f->seq[i]) {
+ int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+ ++sum[c == path[f->vpos + i]? 0 : 1];
+ }
+ left[i] = sum[1]<<16 | sum[0];
+ }
+ for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts
+ if (f->seq[i]) {
+ int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+ ++sum[c == path[f->vpos + i]? 0 : 1];
+ }
+ rght[i] = sum[1]<<16 | sum[0];
+ }
+ // find the best flip point
+ for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) {
+ int a[2];
+ a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY;
+ a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY;
+ if (a[0] > a[1]) {
+ if (a[0] > m) m = a[0], md = 0, mi = i;
+ } else {
+ if (a[1] > m) m = a[1], md = 1, mi = i;
+ }
+ }
+ if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip
+ f->flip = 1;
+ if (md == 0) { // flip the tail
+ for (i = mi + 1; i < f->vlen; ++i)
+ if (f->seq[i] == 1) f->seq[i] = 2;
+ else if (f->seq[i] == 2) f->seq[i] = 1;
+ } else { // flip the head
+ for (i = 0; i <= mi; ++i)
+ if (f->seq[i] == 1) f->seq[i] = 2;
+ else if (f->seq[i] == 2) f->seq[i] = 1;
+ }
+ }
+ }
+ // update pcnt[]
+ if (!f->single) {
+ for (i = 0; i < f->vlen; ++i) {
+ int c;
+ if (f->seq[i] == 0) continue;
+ c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+ if (c == path[f->vpos + i]) {
+ if (f->phase == 0) ++pcnt[f->vpos + i];
+ else pcnt[f->vpos + i] += 1ull<<32;
+ } else {
+ if (f->phase == 0) pcnt[f->vpos + i] += 1<<16;
+ else pcnt[f->vpos + i] += 1ull<<48;
+ }
+ }
+ }
+ }
+ }
+ free(left); free(rght);
+ return pcnt;
+}
+
+static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n)
+{
+ int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0;
+ uint64_t *list = 0;
+ for (i = 0; i < vpos; ++i) {
+ uint64_t x = pcnt[i];
+ int c[4], pre = score, s;
+ c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff;
+ s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1);
+ if (c[3] > c[2]) s += c[3] - c[2];
+ if (c[1] > c[0]) s += c[1] - c[0];
+ score += s;
+ if (score < 0) score = 0;
+ if (pre == 0 && score > 0) beg = i; // change from zero to non-zero
+ if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) {
+ if (n == m) {
+ m = m? m<<1 : 4;
+ list = realloc(list, m * 8);
+ }
+ list[n++] = (uint64_t)beg<<32 | max_i;
+ i = max_i; // reset i to max_i
+ score = 0;
+ } else if (score > max) max = score, max_i = i;
+ if (score == 0) max = 0;
+ }
+ *_n = n;
+ return list;
+}
+
+// trim heading and tailing ambiguous bases; mark deleted and remove sequence
+static int clean_seqs(int vpos, nseq_t *hash)
+{
+ khint_t k;
+ int ret = 0;
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ int beg, end, i;
+ if (f->vpos >= vpos) {
+ ret = 1;
+ continue;
+ }
+ for (i = 0; i < f->vlen; ++i)
+ if (f->seq[i] != 0) break;
+ beg = i;
+ for (i = f->vlen - 1; i >= 0; --i)
+ if (f->seq[i] != 0) break;
+ end = i + 1;
+ if (end - beg <= 0) kh_del(64, hash, k);
+ else {
+ if (beg != 0) memmove(f->seq, f->seq + beg, end - beg);
+ f->vpos += beg; f->vlen = end - beg;
+ f->single = f->vlen == 1? 1 : 0;
+ }
+ }
+ }
+ return ret;
+}
+
+static void dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash)
+{
+ int i, is_flip, drop_ambi;
+ drop_ambi = g->flag & FLAG_DROP_AMBI;
+ is_flip = (drand48() < 0.5);
+ for (i = 0; i < g->n; ++i) {
+ int end, which;
+ uint64_t key;
+ khint_t k;
+ bam1_t *b = g->b[i];
+ key = X31_hash_string(bam1_qname(b));
+ end = bam_calend(&b->core, bam1_cigar(b));
+ if (end > min_pos) break;
+ k = kh_get(64, hash, key);
+ if (k == kh_end(hash)) which = 3;
+ else {
+ frag_t *f = &kh_val(hash, k);
+ if (f->ambig) which = drop_ambi? 2 : 3;
+ else if (f->phased && f->flip) which = 2;
+ else if (f->phased == 0) which = 3;
+ else { // phased and not flipped
+ char c = 'Y';
+ which = f->phase;
+ bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c);
+ }
+ if (which < 2 && is_flip) which = 1 - which; // increase the randomness
+ }
+ if (which == 3) which = (drand48() < 0.5);
+ bam_write1(g->out[which], b);
+ bam_destroy1(b);
+ g->b[i] = 0;
+ }
+ memmove(g->b, g->b + i, (g->n - i) * sizeof(void*));
+ g->n -= i;
+}
+
+static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash)
+{
+ int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos;
+ khint_t k;
+ frag_t **seqs;
+ int8_t *path, *sitemask;
+ uint64_t *pcnt, *regmask;
+
+ if (vpos == 0) return 0;
+ i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos
+ min_pos = i? cns[vpos]>>32 : 0x7fffffff;
+ if (vpos == 1) {
+ printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1);
+ printf("M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1,
+ "ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1);
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos) continue;
+ f->flip = 0;
+ if (f->seq[0] == 0) f->phased = 0;
+ else f->phased = 1, f->phase = f->seq[0] - 1;
+ }
+ }
+ dump_aln(g, min_pos, hash);
+ ++g->vpos_shift;
+ return 1;
+ }
+ { // phase
+ int **cnt;
+ uint64_t *mask;
+ printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1);
+ sitemask = calloc(vpos, 1);
+ cnt = count_all(g->k, vpos, hash);
+ path = dynaprog(g->k, vpos, cnt);
+ for (i = 0; i < vpos; ++i) free(cnt[i]);
+ free(cnt);
+ pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking
+ mask = genmask(vpos, pcnt, &n_masked);
+ regmask = calloc(n_masked, 8);
+ for (i = 0; i < n_masked; ++i) {
+ regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32;
+ for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j)
+ sitemask[j] = 1;
+ }
+ free(mask);
+ if (g->flag & FLAG_FIX_CHIMERA) {
+ free(pcnt);
+ pcnt = fragphase(vpos, path, hash, 1);
+ }
+ }
+ for (i = 0; i < n_masked; ++i)
+ printf("FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1);
+ for (i = 0; i < vpos; ++i) {
+ uint64_t x = pcnt[i];
+ int8_t c[2];
+ c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3);
+ c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3);
+ printf("M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]],
+ i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff));
+ }
+ free(path); free(pcnt); free(regmask); free(sitemask);
+ seqs = calloc(n_seqs, sizeof(void*));
+ for (k = 0, i = 0; k < kh_end(hash); ++k)
+ if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single)
+ seqs[i++] = &kh_val(hash, k);
+ n_seqs = i;
+ ks_introsort_rseq(n_seqs, seqs);
+ for (i = 0; i < n_seqs; ++i) {
+ frag_t *f = seqs[i];
+ printf("EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen);
+ for (j = 0; j < f->vlen; ++j) {
+ uint32_t c = cns[f->vpos + j];
+ if (f->seq[j] == 0) putchar('N');
+ else putchar("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)]);
+ }
+ printf("\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1);
+ }
+ free(seqs);
+ printf("//\n");
+ fflush(stdout);
+ g->vpos_shift += vpos;
+ dump_aln(g, min_pos, hash);
+ return vpos;
+}
+
+static void update_vpos(int vpos, nseq_t *hash)
+{
+ khint_t k;
+ for (k = 0; k < kh_end(hash); ++k) {
+ if (kh_exist(hash, k)) {
+ frag_t *f = &kh_val(hash, k);
+ if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it
+ else f->vpos -= vpos;
+ }
+ }
+}
+
+static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement
+{
+ return hash;
+}
+
+static int readaln(void *data, bam1_t *b)
+{
+ phaseg_t *g = (phaseg_t*)data;
+ int ret;
+ ret = bam_read1(g->fp, b);
+ if (ret < 0) return ret;
+ if (!(b->core.flag & (BAM_FUNMAP|BAM_FSECONDARY|BAM_FQCFAIL|BAM_FDUP)) && g->pre) {
+ if (g->n == g->m) {
+ g->m = g->m? g->m<<1 : 16;
+ g->b = realloc(g->b, g->m * sizeof(void*));
+ }
+ g->b[g->n++] = bam_dup1(b);
+ }
+ return ret;
+}
+
+static khash_t(set64) *loadpos(const char *fn, bam_header_t *h)
+{
+ gzFile fp;
+ kstream_t *ks;
+ int ret, dret;
+ kstring_t *str;
+ khash_t(set64) *hash;
+
+ hash = kh_init(set64);
+ str = calloc(1, sizeof(kstring_t));
+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ int tid = bam_get_tid(h, str->s);
+ if (tid >= 0 && dret != '\n') {
+ if (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
+ kh_put(set64, hash, x, &ret);
+ } else break;
+ }
+ if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+ if (dret < 0) break;
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ return hash;
+}
+
+static int gl2cns(float q[16])
+{
+ int i, j, min_ij;
+ float min, min2;
+ min = min2 = 1e30; min_ij = -1;
+ for (i = 0; i < 4; ++i) {
+ for (j = i; j < 4; ++j) {
+ if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j];
+ else if (q[i<<2|j] < min2) min2 = q[i<<2|j];
+ }
+ }
+ return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2;
+}
+
+int main_phase(int argc, char *argv[])
+{
+ extern void bam_init_header_hash(bam_header_t *header);
+ int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0;
+ const bam_pileup1_t *plp;
+ bam_plp_t iter;
+ bam_header_t *h;
+ nseq_t *seqs;
+ uint64_t *cns = 0;
+ phaseg_t g;
+ char *fn_list = 0;
+ khash_t(set64) *set = 0;
+ errmod_t *em;
+ uint16_t *bases;
+
+ memset(&g, 0, sizeof(phaseg_t));
+ g.flag = FLAG_FIX_CHIMERA;
+ g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256;
+ while ((c = getopt(argc, argv, "Q:eFq:k:b:l:D:A:")) >= 0) {
+ switch (c) {
+ case 'D': g.max_depth = atoi(optarg); break;
+ case 'q': g.min_varLOD = atoi(optarg); break;
+ case 'Q': g.min_baseQ = atoi(optarg); break;
+ case 'k': g.k = atoi(optarg); break;
+ case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break;
+ case 'e': g.flag |= FLAG_LIST_EXCL; break;
+ case 'A': g.flag |= FLAG_DROP_AMBI; break;
+ case 'b': g.pre = strdup(optarg); break;
+ case 'l': fn_list = strdup(optarg); break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: samtools phase [options] <in.bam>\n\n");
+ fprintf(pysamerr, "Options: -k INT block length [%d]\n", g.k);
+ fprintf(pysamerr, " -b STR prefix of BAMs to output [null]\n");
+ fprintf(pysamerr, " -q INT min het phred-LOD [%d]\n", g.min_varLOD);
+ fprintf(pysamerr, " -Q INT min base quality in het calling [%d]\n", g.min_baseQ);
+ fprintf(pysamerr, " -D INT max read depth [%d]\n", g.max_depth);
+// fprintf(pysamerr, " -l FILE list of sites to phase [null]\n");
+ fprintf(pysamerr, " -F do not attempt to fix chimeras\n");
+ fprintf(pysamerr, " -A drop reads with ambiguous phase\n");
+// fprintf(pysamerr, " -e do not discover SNPs (effective with -l)\n");
+ fprintf(pysamerr, "\n");
+ return 1;
+ }
+ g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+ h = bam_header_read(g.fp);
+ if (fn_list) { // read the list of sites to phase
+ bam_init_header_hash(h);
+ set = loadpos(fn_list, h);
+ free(fn_list);
+ } else g.flag &= ~FLAG_LIST_EXCL;
+ if (g.pre) { // open BAMs to write
+ char *s = malloc(strlen(g.pre) + 20);
+ strcpy(s, g.pre); strcat(s, ".0.bam"); g.out[0] = bam_open(s, "w");
+ strcpy(s, g.pre); strcat(s, ".1.bam"); g.out[1] = bam_open(s, "w");
+ strcpy(s, g.pre); strcat(s, ".chimera.bam"); g.out[2] = bam_open(s, "w");
+ for (c = 0; c <= 2; ++c) bam_header_write(g.out[c], h);
+ free(s);
+ }
+
+ iter = bam_plp_init(readaln, &g);
+ g.vpos_shift = 0;
+ seqs = kh_init(64);
+ em = errmod_init(1. - 0.83);
+ bases = calloc(g.max_depth, 2);
+ printf("CC\n");
+ printf("CC\tDescriptions:\nCC\n");
+ printf("CC\t CC comments\n");
+ printf("CC\t PS start of a phase set\n");
+ printf("CC\t FL filtered region\n");
+ printf("CC\t M[012] markers; 0 for singletons, 1 for phased and 2 for filtered\n");
+ printf("CC\t EV supporting reads; SAM format\n");
+ printf("CC\t // end of a phase set\nCC\n");
+ printf("CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n");
+ printf("CC\t PS chr phaseSetStart phaseSetEnd\n");
+ printf("CC\t FL chr filterStart filterEnd\n");
+ printf("CC\t M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1\n");
+ printf("CC\nCC\n");
+ fflush(stdout);
+ while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) {
+ int i, k, c, tmp, dophase = 1, in_set = 0;
+ float q[16];
+ if (tid < 0) break;
+ if (tid != lasttid) { // change of chromosome
+ g.vpos_shift = 0;
+ if (lasttid >= 0) {
+ seqs = shrink_hash(seqs);
+ phase(&g, h->target_name[lasttid], vpos, cns, seqs);
+ update_vpos(0x7fffffff, seqs);
+ }
+ lasttid = tid;
+ vpos = 0;
+ }
+ if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1;
+ if (n > g.max_depth) continue; // do not proceed if the depth is too high
+ // fill the bases array and check if there is a variant
+ for (i = k = 0; i < n; ++i) {
+ const bam_pileup1_t *p = plp + i;
+ uint8_t *seq;
+ int q, baseQ, b;
+ if (p->is_del || p->is_refskip) continue;
+ baseQ = bam1_qual(p->b)[p->qpos];
+ if (baseQ < g.min_baseQ) continue;
+ seq = bam1_seq(p->b);
+ b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
+ if (b > 3) continue;
+ q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+ if (q < 4) q = 4;
+ if (q > 63) q = 63;
+ bases[k++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
+ }
+ if (k == 0) continue;
+ errmod_cal(em, k, 4, bases, q); // compute genotype likelihood
+ c = gl2cns(q); // get the consensus
+ // tell if to proceed
+ if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list
+ if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant
+ // add the variant
+ if (vpos == max_vpos) {
+ max_vpos = max_vpos? max_vpos<<1 : 128;
+ cns = realloc(cns, max_vpos * 8);
+ }
+ cns[vpos] = (uint64_t)pos<<32 | c;
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = plp + i;
+ uint64_t key;
+ khint_t k;
+ uint8_t *seq = bam1_seq(p->b);
+ frag_t *f;
+ if (p->is_del || p->is_refskip) continue;
+ if (p->b->core.qual == 0) continue;
+ // get the base code
+ c = nt16_nt4_table[(int)bam1_seqi(seq, p->qpos)];
+ if (c == (cns[vpos]&3)) c = 1;
+ else if (c == (cns[vpos]>>16&3)) c = 2;
+ else c = 0;
+ // write to seqs
+ key = X31_hash_string(bam1_qname(p->b));
+ k = kh_put(64, seqs, key, &tmp);
+ f = &kh_val(seqs, k);
+ if (tmp == 0) { // present in the hash table
+ if (vpos - f->vpos + 1 < MAX_VARS) {
+ f->vlen = vpos - f->vpos + 1;
+ f->seq[f->vlen-1] = c;
+ f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
+ }
+ dophase = 0;
+ } else { // absent
+ memset(f->seq, 0, MAX_VARS);
+ f->beg = p->b->core.pos;
+ f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
+ f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0;
+ }
+ }
+ if (dophase) {
+ seqs = shrink_hash(seqs);
+ phase(&g, h->target_name[tid], vpos, cns, seqs);
+ update_vpos(vpos, seqs);
+ cns[0] = cns[vpos];
+ vpos = 0;
+ }
+ ++vpos;
+ }
+ if (tid >= 0) phase(&g, h->target_name[tid], vpos, cns, seqs);
+ bam_header_destroy(h);
+ bam_plp_destroy(iter);
+ bam_close(g.fp);
+ kh_destroy(64, seqs);
+ kh_destroy(set64, set);
+ free(cns);
+ errmod_destroy(em);
+ free(bases);
+ if (g.pre) {
+ for (c = 0; c <= 2; ++c) bam_close(g.out[c]);
+ free(g.pre); free(g.b);
+ }
+ return 0;
+}
{
samfile_t *fp;
fp = (samfile_t*)calloc(1, sizeof(samfile_t));
- if (mode[0] == 'r') { // read
+ if (strchr(mode, 'r')) { // read
fp->type |= TYPE_READ;
- if (mode[1] == 'b') { // binary
+ if (strchr(mode, 'b')) { // binary
fp->type |= TYPE_BAM;
fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
if (fp->x.bam == 0) goto open_err_ret;
append_header_text(fp->header, textheader->text, textheader->l_text);
bam_header_destroy(textheader);
}
- if (fp->header->n_targets == 0)
+ if (fp->header->n_targets == 0 && bam_verbose >= 1)
fprintf(pysamerr, "[samopen] no @SQ lines in the header.\n");
- } else fprintf(pysamerr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
+ } else if (bam_verbose >= 2) fprintf(pysamerr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
}
- } else if (mode[0] == 'w') { // write
+ } else if (strchr(mode, 'w')) { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
- if (mode[1] == 'b') { // binary
+ if (strchr(mode, 'b')) { // binary
char bmode[3];
- bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
+ int i, compress_level = -1;
+ for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0;
fp->type |= TYPE_BAM;
fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
if (fp->x.bam == 0) goto open_err_ret;
// open file
fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
if (fp->x.tamr == 0) goto open_err_ret;
- if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
- else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
+ if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
+ else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
else fp->type |= BAM_OFDEC<<2;
// write header
- if (strstr(mode, "h")) {
+ if (strchr(mode, 'h')) {
int i;
bam_header_t *alt;
// parse the header text
sam_header_parse(alt);
alt->l_text = 0; alt->text = 0;
// check if there are @SQ lines in the header
- fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
+ fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL
if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
- if (alt->n_targets != fp->header->n_targets)
- fprintf(pysamerr, "[samopen] inconsistent number of target sequences.\n");
+ if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1)
+ fprintf(pysamerr, "[samopen] inconsistent number of target sequences. Output the text header.\n");
} else { // then dump ->target_{name,len}
for (i = 0; i < fp->header->n_targets; ++i)
fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
if (access(fn_ref, R_OK) == -1) {
fprintf(pysamerr, "[samfaipath] fail to read file %s.\n", fn_ref);
} else {
- fprintf(pysamerr, "[samfaipath] build FASTA index...\n");
+ if (bam_verbose >= 3) fprintf(pysamerr, "[samfaipath] build FASTA index...\n");
if (fai_build(fn_ref) == -1) {
fprintf(pysamerr, "[samfaipath] fail to build FASTA index.\n");
free(fn_list); fn_list = 0;
const char *r_sq_tags[] = {"SN","LN",NULL};
const char *u_sq_tags[] = {"SN",NULL};
-const char *o_rg_tags[] = {"LB","DS","PU","PI","CN","DT","PL",NULL};
+const char *o_rg_tags[] = {"CN","DS","DT","FO","KS","LB","PG","PI","PL","PU","SM",NULL};
const char *r_rg_tags[] = {"ID",NULL};
const char *u_rg_tags[] = {"ID",NULL};
const char *text;
char *buf=NULL;
size_t nbuf = 0;
+ int tovalidate = 0;
if ( !headerText )
return 0;
while ( (text=nextline(&buf, &nbuf, text)) )
{
hline = sam_header_line_parse(buf);
- if ( hline && sam_header_line_validate(hline) )
+ if ( hline && (!tovalidate || sam_header_line_validate(hline)) )
// With too many (~250,000) reference sequences the header parsing was too slow with list_append.
hlines = list_append_to_end(hlines, hline);
else
#include "sam_header.h"
#include "sam.h"
#include "faidx.h"
+#include "kstring.h"
#include "khash.h"
KHASH_SET_INIT_STR(rg)
typedef khash_t(rg) *rghash_t;
-rghash_t g_rghash = 0;
+static rghash_t g_rghash = 0;
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
static char *g_library, *g_rg;
static int g_sol2sanger_tbl[128];
+static void *g_bed;
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
static void sol2sanger(bam1_t *b)
{
{
if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
return 1;
+ if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
+ return 1;
if (g_rg || g_rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
return 0;
}
+static char *drop_rg(char *hdtxt, rghash_t h, int *len)
+{
+ char *p = hdtxt, *q, *r, *s;
+ kstring_t str;
+ memset(&str, 0, sizeof(kstring_t));
+ while (1) {
+ int toprint = 0;
+ q = strchr(p, '\n');
+ if (q == 0) q = p + strlen(p);
+ if (q - p < 3) break; // the line is too short; then stop
+ if (strncmp(p, "@RG\t", 4) == 0) {
+ int c;
+ khint_t k;
+ if ((r = strstr(p, "\tID:")) != 0) {
+ r += 4;
+ for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
+ c = *s; *s = '\0';
+ k = kh_get(rg, h, r);
+ *s = c;
+ if (k != kh_end(h)) toprint = 1;
+ }
+ } else toprint = 1;
+ if (toprint) {
+ kputsn(p, q - p, &str); kputc('\n', &str);
+ }
+ p = q + 1;
+ }
+ *len = str.l;
+ return str.s;
+}
+
// callback function for bam_fetch() that prints nonskipped records
static int view_func(const bam1_t *b, void *data)
{
int main_samview(int argc, char *argv[])
{
- int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0, is_count = 0;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 0;
int of_type = BAM_OFDEC, is_long_help = 0;
int count = 0;
samfile_t *in = 0, *out = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbct:hHo:q:f:F:ul:r:xX?T:CR:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 0) {
switch (c) {
case 'c': is_count = 1; break;
case 'C': slx2sngr = 1; break;
case 'f': g_flag_on = strtol(optarg, 0, 0); break;
case 'F': g_flag_off = strtol(optarg, 0, 0); break;
case 'q': g_min_mapQ = atoi(optarg); break;
- case 'u': is_uncompressed = 1; break;
+ case 'u': compress_level = 0; break;
+ case '1': compress_level = 1; break;
case 'l': g_library = strdup(optarg); break;
+ case 'L': g_bed = bed_read(optarg); break;
case 'r': g_rg = strdup(optarg); break;
case 'R': fn_rg = strdup(optarg); break;
case 'x': of_type = BAM_OFHEX; break;
default: return usage(is_long_help);
}
}
- if (is_uncompressed) is_bamout = 1;
+ if (compress_level >= 0) is_bamout = 1;
if (is_header_only) is_header = 1;
if (is_bamout) strcat(out_mode, "b");
else {
}
if (is_bamin) strcat(in_mode, "b");
if (is_header) strcat(out_mode, "h");
- if (is_uncompressed) strcat(out_mode, "u");
+ if (compress_level >= 0) {
+ char tmp[2];
+ tmp[0] = compress_level + '0'; tmp[1] = '\0';
+ strcat(out_mode, tmp);
+ }
if (argc == optind) return usage(is_long_help); // potential memory leak...
// read the list of read groups
ret = 1;
goto view_end;
}
+ if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
+ char *tmp;
+ int l;
+ tmp = drop_rg(in->header->text, g_rghash, &l);
+ free(in->header->text);
+ in->header->text = tmp;
+ in->header->l_text = l;
+ }
if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
fprintf(pysamerr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
ret = 1;
}
// close files, free and return
free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
+ if (g_bed) bed_destroy(g_bed);
if (g_rghash) {
khint_t k;
for (k = 0; k < kh_end(g_rghash); ++k)
fprintf(pysamerr, " -H print header only (no alignments)\n");
fprintf(pysamerr, " -S input is SAM\n");
fprintf(pysamerr, " -u uncompressed BAM output (force -b)\n");
+ fprintf(pysamerr, " -1 fast compression (force -b)\n");
fprintf(pysamerr, " -x output FLAG in HEX (samtools-C specific)\n");
fprintf(pysamerr, " -X output FLAG in string (samtools-C specific)\n");
fprintf(pysamerr, " -c print only the count of matching records\n");
+ fprintf(pysamerr, " -L FILE output alignments overlapping the input BED FILE [null]\n");
fprintf(pysamerr, " -t FILE list of reference names and lengths (force -S) [null]\n");
fprintf(pysamerr, " -T FILE reference sequence file (force -S) [null]\n");
fprintf(pysamerr, " -o FILE output file name [stdout]\n");
++n;
}
if (n == 0) add_pair(sm, sm2id, fn, fn);
+// add_pair(sm, sm2id, fn, fn);
free(buf.s);
return 0;
}
[bdist_rpm]
-vendor = TDB
doc_files = README doc/*.html ChangeLog
-distribution-name = Red Hat Linux
+vendor = TDB
packager = TDB <email@email.com>
+distribution-name = Red Hat Linux
requires = python
[egg_info]
'''
import os, sys, glob, shutil, hashlib, re, fnmatch
+import platform
name = "pysam"
for filename in fnmatch.filter(files, pattern):
yield os.path.join(path, filename)
+def _update_pysam_files(cf, destdir):
+ for filename in cf:
+ if not filename: continue
+ dest = filename + ".pysam.c"
+ with open( filename ) as infile:
+ with open( dest, "w" ) as outfile:
+ outfile.write( '#include "pysam.h"\n\n' )
+ outfile.write( re.sub( "stderr", "pysamerr", "".join(infile.readlines()) ) )
+ with open( os.path.join( destdir, "pysam.h" ), "w" )as outfile:
+ outfile.write ("""#ifndef PYSAM_H
+#define PYSAM_H
+#include "stdio.h"
+extern FILE * pysamerr;
+#endif
+""")
# copy samtools source
if len(sys.argv) >= 2 and sys.argv[1] == "import":
print "installed latest source code from %s: %i files copied" % (srcdir, ncopied)
# redirect stderr to pysamerr and replace bam.h with a stub.
print "applying stderr redirection"
+
+ _update_pysam_files(cf, destdir)
- for filename in cf:
- if not filename: continue
- dest = filename + ".pysam.c"
- with open( filename ) as infile:
- with open( dest, "w" ) as outfile:
- outfile.write( '#include "pysam.h"\n\n' )
- outfile.write( re.sub( "stderr", "pysamerr", "".join(infile.readlines()) ) )
-
- with open( os.path.join( destdir, "pysam.h" ), "w" )as outfile:
- outfile.write ("""#ifndef PYSAM_H
-#define PYSAM_H
-#include "stdio.h"
-extern FILE * pysamerr;
-#endif
-""")
sys.exit(0)
+if len(sys.argv) >= 2 and sys.argv[1] == "refresh":
+ print "refreshing latest source code from .c to .pysam.c"
+# redirect stderr to pysamerr and replace bam.h with a stub.
+ print "applying stderr redirection"
+ for destdir in ('samtools', 'tabix'):
+ pysamcfiles = locate( "*.pysam.c", destdir )
+ for f in pysamcfiles: os.remove(f)
+ cfiles = locate( "*.c", destdir )
+ _update_pysam_files(cfiles, destdir)
+
+ sys.exit(0)
+
+
+
from ez_setup import use_setuptools
use_setuptools()
Topic :: Scientific/Engineering :: Bioinformatics
"""
+if platform.system()=='Windows':
+ include_os = ['win32']
+ os_c_files = ['win32/getopt.c']
+else:
+ include_os = []
+ os_c_files = []
+
samtools = Extension(
"csamtools", # name of extension
[ "pysam/csamtools.pyx" ] +\
[ "pysam/%s" % x for x in (
"pysam_util.c", )] +\
glob.glob( os.path.join( "samtools", "*.pysam.c" )) +\
+ os_c_files + \
glob.glob( os.path.join( "samtools", "*", "*.pysam.c" ) ),
library_dirs=[],
- include_dirs=[ "samtools", "pysam" ],
+ include_dirs=[ "samtools", "pysam" ] + include_os,
libraries=[ "z", ],
language="c",
define_macros = [('_FILE_OFFSET_BITS','64'),
tabix = Extension(
"ctabix", # name of extension
- [ "pysam/ctabix.pyx" ] +\
+ [ "pysam/ctabix.pyx", ] +\
[ "pysam/%s" % x for x in ( "tabix_util.c", )] +\
+ os_c_files + \
glob.glob( os.path.join( "tabix", "*.pysam.c" ) ),
library_dirs=[],
- include_dirs=[ "tabix", "pysam" ],
+ include_dirs=[ "tabix", "pysam" ] + include_os,
+ libraries=[ "z", ],
+ language="c",
+ )
+
+tabproxies = Extension(
+ "TabProxies", # name of extension
+ [ "pysam/TabProxies.pyx", ] + os_c_files,
+ library_dirs=[],
+ include_dirs= include_os,
+ libraries=[ "z", ],
+ language="c",
+ )
+
+cvcf = Extension(
+ "cvcf", # name of extension
+ [ "pysam/cvcf.pyx", ] + os_c_files,
+ library_dirs=[],
+ include_dirs= ["tabix",] + include_os,
libraries=[ "z", ],
language="c",
)
"pysam/namedtuple",
"pysam/version" ],
'requires' : ['cython (>=0.12)'],
- 'ext_modules': [samtools, tabix],
+ 'ext_modules': [samtools, tabix, tabproxies, cvcf ],
'cmdclass' : {'build_ext': build_ext},
'install_requires' : ['cython>=0.12.1',],
+ # do not pack in order to permit linking to csamtools.so
+ 'zip_safe' :False,
}
if __name__=='__main__':
--- /dev/null
+#include "pysam.h"
+
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+
+#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);
+}
fp->error = message;
}
-int is_bgzipped(const char *fn)
+int bgzf_check_bgzf(const char *fn)
{
BGZF *fp;
uint8_t buf[10],magic[10]="\037\213\010\4\0\0\0\0\0\377";
if ((fp = bgzf_open(fn, "r")) == 0)
{
- fprintf(pysamerr, "[is_bgzipped] failed to open the file: %s\n",fn);
+ fprintf(pysamerr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
return -1;
}
static
BGZF*
-open_write(int fd, bool is_uncompressed)
+open_write(int fd, int compress_level) // compress_level==-1 for the default level
{
FILE* file = fdopen(fd, "w");
BGZF* fp;
fp = malloc(sizeof(BGZF));
fp->file_descriptor = fd;
fp->open_mode = 'w';
- fp->owned_file = 0; fp->is_uncompressed = is_uncompressed;
+ fp->owned_file = 0;
+ 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;
#ifdef _USE_KNETFILE
fp->x.fpw = file;
#else
bgzf_open(const char* __restrict path, const char* __restrict mode)
{
BGZF* fp = NULL;
- if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */
+ if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
#ifdef _USE_KNETFILE
knetFile *file = knet_open(path, mode);
if (file == 0) return 0;
if (fd == -1) return 0;
fp = open_read(fd);
#endif
- } else if (mode[0] == 'w' || mode[0] == 'W') {
- int fd, oflag = O_WRONLY | O_CREAT | O_TRUNC;
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
#ifdef _WIN32
oflag |= O_BINARY;
#endif
fd = open(path, oflag, 0666);
if (fd == -1) return 0;
- fp = open_write(fd, strstr(mode, "u")? 1 : 0);
- }
- if (fp != NULL) {
- fp->owned_file = 1;
+ { // set compress_level
+ int i;
+ 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;
+ }
+ fp = open_write(fd, compress_level);
}
+ if (fp != NULL) fp->owned_file = 1;
return fp;
}
if (mode[0] == 'r' || mode[0] == 'R') {
return open_read(fd);
} else if (mode[0] == 'w' || mode[0] == 'W') {
- return open_write(fd, strstr(mode, "u")? 1 : 0);
+ 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 open_write(fd, compress_level);
} else {
return NULL;
}
int input_length = block_length;
int compressed_length = 0;
while (1) {
- int compress_level = fp->is_uncompressed? 0 : Z_DEFAULT_COMPRESSION;
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
- int status = deflateInit2(&zs, compress_level, Z_DEFLATED,
+ int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED,
GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
if (status != Z_OK) {
report_error(fp, "deflate init failed");
// Inflate the block in fp->compressed_block into fp->uncompressed_block
z_stream zs;
+ int status;
zs.zalloc = NULL;
zs.zfree = NULL;
zs.next_in = fp->compressed_block + 18;
zs.next_out = fp->uncompressed_block;
zs.avail_out = fp->uncompressed_block_size;
- int status = inflateInit2(&zs, GZIP_WINDOW_BITS);
+ status = inflateInit2(&zs, GZIP_WINDOW_BITS);
if (status != Z_OK) {
report_error(fp, "inflate init failed");
return -1;
bgzf_read_block(BGZF* fp)
{
bgzf_byte_t header[BLOCK_HEADER_LENGTH];
- int size = 0;
+ int count, size = 0, block_length, remaining;
#ifdef _USE_KNETFILE
int64_t block_address = knet_tell(fp->x.fpr);
if (load_block_from_cache(fp, block_address)) return 0;
- int count = knet_read(fp->x.fpr, header, sizeof(header));
+ count = knet_read(fp->x.fpr, header, sizeof(header));
#else
int64_t block_address = ftello(fp->file);
if (load_block_from_cache(fp, block_address)) return 0;
- int count = fread(header, 1, sizeof(header), fp->file);
+ count = fread(header, 1, sizeof(header), fp->file);
#endif
if (count == 0) {
fp->block_length = 0;
report_error(fp, "invalid block header");
return -1;
}
- int block_length = unpackInt16((uint8_t*)&header[16]) + 1;
+ block_length = unpackInt16((uint8_t*)&header[16]) + 1;
bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
- int remaining = block_length - BLOCK_HEADER_LENGTH;
+ remaining = block_length - BLOCK_HEADER_LENGTH;
#ifdef _USE_KNETFILE
count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
#else
}
size += count;
count = inflate_block(fp, block_length);
- if (count < 0) {
- return -1;
- }
+ if (count < 0) return -1;
if (fp->block_length != 0) {
// Do not reset offset if this read follows a seek.
fp->block_offset = 0;
int bytes_read = 0;
bgzf_byte_t* output = data;
while (bytes_read < length) {
- int available = fp->block_length - fp->block_offset;
+ int copy_length, available = fp->block_length - fp->block_offset;
+ bgzf_byte_t *buffer;
if (available <= 0) {
if (bgzf_read_block(fp) != 0) {
return -1;
break;
}
}
- int copy_length = bgzf_min(length-bytes_read, available);
- bgzf_byte_t* buffer = fp->uncompressed_block;
+ copy_length = bgzf_min(length-bytes_read, available);
+ buffer = fp->uncompressed_block;
memcpy(output, buffer + fp->block_offset, copy_length);
fp->block_offset += copy_length;
output += copy_length;
return bytes_read;
}
-static
-int
-flush_block(BGZF* fp)
+int bgzf_flush(BGZF* fp)
{
while (fp->block_offset > 0) {
- int block_length = deflate_block(fp, fp->block_offset);
- if (block_length < 0) {
- return -1;
- }
+ int count, block_length;
+ block_length = deflate_block(fp, fp->block_offset);
+ if (block_length < 0) return -1;
#ifdef _USE_KNETFILE
- int count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
+ count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
#else
- int count = fwrite(fp->compressed_block, 1, block_length, fp->file);
+ count = fwrite(fp->compressed_block, 1, block_length, fp->file);
#endif
if (count != block_length) {
report_error(fp, "write failed");
return 0;
}
-int
-bgzf_write(BGZF* fp, const void* data, int length)
+int bgzf_flush_try(BGZF *fp, int size)
{
+ if (fp->block_offset + size > fp->uncompressed_block_size)
+ return bgzf_flush(fp);
+ return -1;
+}
+
+int bgzf_write(BGZF* fp, const void* data, int length)
+{
+ const bgzf_byte_t *input = data;
+ int block_length, bytes_written;
if (fp->open_mode != 'w') {
report_error(fp, "file not open for writing");
return -1;
}
- if (fp->uncompressed_block == NULL) {
+ if (fp->uncompressed_block == NULL)
fp->uncompressed_block = malloc(fp->uncompressed_block_size);
- }
- const bgzf_byte_t* input = data;
- int block_length = fp->uncompressed_block_size;
- int bytes_written = 0;
+ input = data;
+ block_length = fp->uncompressed_block_size;
+ bytes_written = 0;
while (bytes_written < length) {
int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
bgzf_byte_t* buffer = fp->uncompressed_block;
input += copy_length;
bytes_written += copy_length;
if (fp->block_offset == block_length) {
- if (flush_block(fp) != 0) {
+ if (bgzf_flush(fp) != 0) {
break;
}
}
return bytes_written;
}
-int
-bgzf_close(BGZF* fp)
+int bgzf_close(BGZF* fp)
{
if (fp->open_mode == 'w') {
- if (flush_block(fp) != 0) {
- return -1;
- }
+ if (bgzf_flush(fp) != 0) return -1;
{ // add an empty block
int count, block_length = deflate_block(fp, 0);
#ifdef _USE_KNETFILE
else ret = knet_close(fp->x.fpr);
if (ret != 0) return -1;
#else
- if (fclose(fp->file) != 0) {
- return -1;
- }
+ if (fclose(fp->file) != 0) return -1;
#endif
}
free(fp->uncompressed_block);
return (memcmp(magic, buf, 28) == 0)? 1 : 0;
}
-int64_t
-bgzf_seek(BGZF* fp, int64_t pos, int where)
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
{
+ int block_offset;
+ int64_t block_address;
+
if (fp->open_mode != 'r') {
report_error(fp, "file not open for read");
return -1;
report_error(fp, "unimplemented seek option");
return -1;
}
- int block_offset = pos & 0xFFFF;
- int64_t block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
+ block_offset = pos & 0xFFFF;
+ block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
#ifdef _USE_KNETFILE
if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
#else
#include <stdint.h>
#include <stdio.h>
-#include <stdbool.h>
#include <zlib.h>
#ifdef _USE_KNETFILE
#include "knetfile.h"
typedef struct {
int file_descriptor;
char open_mode; // 'r' or 'w'
- bool owned_file, is_uncompressed;
+ int16_t owned_file, compress_level;
#ifdef _USE_KNETFILE
union {
knetFile *fpr;
extern "C" {
#endif
-/*
- * Checks the magic string of the file. Returns 1
- * for bgzipped files, -1 on errors and 0 for files
- * without the bgzip magic string.
- */
-int is_bgzipped(const char *path);
-
/*
* Open an existing file descriptor for reading or writing.
* Mode must be either "r" or "w".
void bgzf_set_cache_size(BGZF *fp, int cache_size);
int bgzf_check_EOF(BGZF *fp);
-
int bgzf_read_block(BGZF* fp);
+int bgzf_flush(BGZF* fp);
+int bgzf_flush_try(BGZF *fp, int size);
+int bgzf_check_bgzf(const char *fn);
#ifdef __cplusplus
}
return tid;
}
-static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
+int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv)
{
- int i, b = 0, id = 1;
+ int i, b = 0, id = 1, ncols = 0;
char *s;
- intv->tid = intv->beg = intv->end = intv->bin = -1;
- for (i = 0; i <= str->l; ++i) {
- if (str->s[i] == '\t' || str->s[i] == 0) {
- if (id == idx->conf.sc) {
- str->s[i] = 0;
- intv->tid = get_tid(idx, str->s + b);
- if (i != str->l) str->s[i] = '\t';
- } else if (id == idx->conf.bc) {
+ 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(str->s + b, &s, 0);
- if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
+ 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 ((idx->conf.preset&0xffff) == TI_PRESET_GENERIC) {
- if (id == idx->conf.ec) intv->end = strtol(str->s + b, &s, 0);
- } else if ((idx->conf.preset&0xffff) == TI_PRESET_SAM) {
+ 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 = str->s + b; s < str->s + i;) {
+ 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;
if (l == 0) l = 1;
intv->end = intv->beg + l;
}
- } else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
+ } 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 = str->s[i];
- str->s[i] = 0;
- s = strstr(str->s + b, "END=");
- if (s == str->s + b) s += 4;
+ int c = line[i];
+ line[i] = 0;
+ s = strstr(line + b, "END=");
+ if (s == line + b) s += 4;
else if (s) {
- s = strstr(str->s + b, ";END=");
+ s = strstr(line + b, ";END=");
if (s) s += 5;
}
if (s) intv->end = strtol(s, &s, 0);
- str->s[i] = c;
+ line[i] = c;
}
}
}
++id;
}
}
- if (intv->tid < 0 || intv->beg < 0 || intv->end < 0) return -1;
- intv->bin = ti_reg2bin(intv->beg, intv->end);
+/*
+ if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) {
+ if (ncols == 1) fprintf(pysamerr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line);
+ else fprintf(pysamerr,"[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(pysamerr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s);
+ return -1;
+ }
+}
+
/************
* indexing *
************/
continue;
}
get_intv(idx, str, &intv);
+ if ( intv.beg<0 || intv.end<0 )
+ {
+ fprintf(pysamerr,"[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(pysamerr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted?\n",(unsigned long long)lineno);
+ fprintf(pysamerr,"[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;
return 0;
}
+const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; }
+
/*******************
* High-level APIs *
*******************/
--- /dev/null
+/* 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 <lh3@sanger.ac.uk> */
+
+/*
+ 2009-07-16 (lh3): in kstream_t, change "char*" to "unsigned char*"
+ */
+
+/* Last Modified: 12APR2009 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB 1 // isspace() && !' '
+#define KS_SEP_MAX 1
+
+#define __KS_TYPE(type_t) \
+ typedef struct __kstream_t { \
+ unsigned char *buf; \
+ int begin, end, is_eof; \
+ type_t f; \
+ } kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(type_t, __bufsize) \
+ static inline kstream_t *ks_init(type_t f) \
+ { \
+ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
+ ks->f = f; \
+ ks->buf = malloc(__bufsize); \
+ return ks; \
+ } \
+ static inline void ks_destroy(kstream_t *ks) \
+ { \
+ if (ks) { \
+ free(ks->buf); \
+ free(ks); \
+ } \
+ }
+
+#define __KS_GETC(__read, __bufsize) \
+ static inline int ks_getc(kstream_t *ks) \
+ { \
+ if (ks->is_eof && ks->begin >= ks->end) return -1; \
+ if (ks->begin >= ks->end) { \
+ ks->begin = 0; \
+ ks->end = __read(ks->f, ks->buf, __bufsize); \
+ if (ks->end < __bufsize) ks->is_eof = 1; \
+ if (ks->end == 0) return -1; \
+ } \
+ return (int)ks->buf[ks->begin++]; \
+ }
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize) \
+ static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+ { \
+ if (dret) *dret = 0; \
+ str->l = 0; \
+ if (ks->begin >= ks->end && ks->is_eof) return -1; \
+ for (;;) { \
+ int i; \
+ if (ks->begin >= ks->end) { \
+ if (!ks->is_eof) { \
+ ks->begin = 0; \
+ ks->end = __read(ks->f, ks->buf, __bufsize); \
+ if (ks->end < __bufsize) ks->is_eof = 1; \
+ if (ks->end == 0) break; \
+ } else break; \
+ } \
+ if (delimiter > KS_SEP_MAX) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (ks->buf[i] == delimiter) break; \
+ } else if (delimiter == KS_SEP_SPACE) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (isspace(ks->buf[i])) break; \
+ } else if (delimiter == KS_SEP_TAB) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
+ } else i = 0; /* never come to here! */ \
+ if (str->m - str->l < i - ks->begin + 1) { \
+ str->m = str->l + (i - ks->begin) + 1; \
+ kroundup32(str->m); \
+ str->s = (char*)realloc(str->s, str->m); \
+ } \
+ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
+ str->l = str->l + (i - ks->begin); \
+ ks->begin = i + 1; \
+ if (i < ks->end) { \
+ if (dret) *dret = ks->buf[i]; \
+ break; \
+ } \
+ } \
+ if (str->l == 0) { \
+ str->m = 1; \
+ str->s = (char*)calloc(1, 1); \
+ } \
+ str->s[str->l] = '\0'; \
+ return str->l; \
+ }
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
+ __KS_TYPE(type_t) \
+ __KS_BASIC(type_t, __bufsize) \
+ __KS_GETC(__read, __bufsize) \
+ __KS_GETUNTIL(__read, __bufsize)
+
+#define __KSEQ_BASIC(type_t) \
+ static inline kseq_t *kseq_init(type_t fd) \
+ { \
+ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
+ s->f = ks_init(fd); \
+ return s; \
+ } \
+ static inline void kseq_rewind(kseq_t *ks) \
+ { \
+ ks->last_char = 0; \
+ ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
+ } \
+ static inline void kseq_destroy(kseq_t *ks) \
+ { \
+ if (!ks) return; \
+ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
+ ks_destroy(ks->f); \
+ free(ks); \
+ }
+
+/* Return value:
+ >=0 length of the sequence (normal)
+ -1 end-of-file
+ -2 truncated quality string
+ */
+#define __KSEQ_READ \
+ static int kseq_read(kseq_t *seq) \
+ { \
+ int c; \
+ kstream_t *ks = seq->f; \
+ if (seq->last_char == 0) { /* then jump to the next header line */ \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
+ if (c == -1) return -1; /* end of file */ \
+ seq->last_char = c; \
+ } /* the first header char has been read */ \
+ seq->comment.l = seq->seq.l = seq->qual.l = 0; \
+ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \
+ if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+ if (isgraph(c)) { /* printable non-space character */ \
+ if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
+ seq->seq.m = seq->seq.l + 2; \
+ kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
+ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+ } \
+ seq->seq.s[seq->seq.l++] = (char)c; \
+ } \
+ } \
+ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
+ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
+ if (c != '+') return seq->seq.l; /* FASTA */ \
+ if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \
+ seq->qual.m = seq->seq.m; \
+ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
+ } \
+ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+ if (c == -1) return -2; /* we should not stop here */ \
+ while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \
+ if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \
+ seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \
+ seq->last_char = 0; /* we have not come to the next header line */ \
+ if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
+ return seq->seq.l; \
+ }
+
+#define __KSEQ_TYPE(type_t) \
+ typedef struct { \
+ kstring_t name, comment, seq, qual; \
+ int last_char; \
+ kstream_t *f; \
+ } kseq_t;
+
+#define KSEQ_INIT(type_t, __read) \
+ KSTREAM_INIT(type_t, __read, 4096) \
+ __KSEQ_TYPE(type_t) \
+ __KSEQ_BASIC(type_t) \
+ __KSEQ_READ
+
+#endif
--- /dev/null
+// Windows-specific code, include with:\r
+// #ifdef _MSC_VER\r
+// #include <msvc_compat.h>\r
+// #endif\r
+\r
+//#define _CRT_SECURE_NO_WARNINGS\r
+#ifndef MSVC_COMPAT_H\r
+#define MSVC_COMPAT_H\r
+\r
+#define inline __inline\r
+#define __func__ __FUNCTION__\r
+\r
+#include <float.h>\r
+#define isnan _isnan\r
+static int isinf(double x) {\r
+ int y = _finite(x);\r
+ if(y == 0) {\r
+ return 0;\r
+ } else {\r
+ return 1;\r
+ }\r
+}\r
+#define alloca _alloca\r
+#define atoll _atoi64\r
+\r
+#define ftello ftell\r
+
+typedef int bool;\r
+\r
+static int R_OK = 4;
+\r
+#ifndef lgamma\r
+/* Log gamma function\r
+ * \log{\Gamma(z)}\r
+ * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245\r
+ */\r
+static double lgamma(double z)\r
+{\r
+ double x = 0;\r
+ x += 0.1659470187408462e-06 / (z+7);\r
+ x += 0.9934937113930748e-05 / (z+6);\r
+ x -= 0.1385710331296526 / (z+5);\r
+ x += 12.50734324009056 / (z+4);\r
+ x -= 176.6150291498386 / (z+3);\r
+ x += 771.3234287757674 / (z+2);\r
+ x -= 1259.139216722289 / (z+1);\r
+ x += 676.5203681218835 / z;\r
+ x += 0.9999999999995183;\r
+ return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);\r
+}\r
+#endif\r
+\r
+#ifndef M_LN10\r
+#define M_LN10 2.30258509299404568402\r
+#endif\r
+#ifndef M_LN2\r
+#define M_LN2 0.69314718055994530942\r
+#endif\r
+
+#endif\r
int32_t meta_char, line_skip;
} ti_conf_t;
+typedef struct {
+ int beg, end;
+ char *ss, *se;
+} ti_interval_t;
+
extern ti_conf_t ti_conf_gff, ti_conf_bed, ti_conf_psltbl, ti_conf_vcf, ti_conf_sam; // preset
#ifdef __cplusplus
/* Get the data line pointed by the iterator and iterate to the next record. */
const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len);
+ const ti_conf_t *ti_get_conf(ti_index_t *idx);
+ int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv);
+
/*******************
* Deprecated APIs *
*******************/
pysam_method, pysam_options = pysam_command
output = pysam_method( *pysam_options.split(" "), raw=True)
if ">" in samtools_command:
- outfile = open( pysam_target, "w" )
+ outfile = open( pysam_target, "wb" )
for line in output: outfile.write( line )
outfile.close()
def _r( s ):
# patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a -> 0.1.12
+ if s.count('-') > 0: s = s[0:s.find('-')]
return re.sub( "[^0-9.]", "", s )
if _r(samtools_version) != _r( pysam.__samtools_version__):
self.assertRaises( ValueError, samfile.pileup, 'chr1', 100, 120)
self.assertRaises( ValueError, samfile.getrname, 0 )
self.assertRaises( ValueError, samfile.tell )
- self.assertRaises( ValueError, samfile.write, None )
self.assertRaises( ValueError, samfile.seek, 0 )
self.assertRaises( ValueError, getattr, samfile, "nreferences" )
self.assertRaises( ValueError, getattr, samfile, "references" )
self.assertRaises( ValueError, getattr, samfile, "text" )
self.assertRaises( ValueError, getattr, samfile, "header" )
- def testBinaryReadFromSamfile( self ):
- pass
- # needs to re-activated, see issue 19
- #samfile = pysam.Samfile( "ex1.bam", "r" )
- #samfile.fetch().next()
+ # write on closed file
+ self.assertEqual( 0, samfile.write(None) )
+
+ def testAutoDetection( self ):
+ samfile = pysam.Samfile( "ex3.bam" )
+ samfile.fetch()
+ samfile.close()
+
+ samfile = pysam.Samfile( "ex3.sam")
+ samfile.fetch()
+ samfile.close()
def testReadingFromFileWithoutIndex( self ):
'''read from bam file without index.'''
self.assertRaises( ValueError, self.samfile.count, region="chr1:-5--10" )
def testOutOfRangNewFormat(self):
- self.assertRaises( OverflowError, self.samfile.fetch, "chr1", 9999999999, 99999999999 )
- self.assertRaises( OverflowError, self.samfile.count, "chr1", 9999999999, 99999999999 )
+ self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999, 99999999999 )
+ self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999, 99999999999 )
def testOutOfRangeLargeNewFormat(self):
- self.assertRaises( OverflowError, self.samfile.fetch, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 )
- self.assertRaises( OverflowError, self.samfile.count, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 )
+ self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 )
+ self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 )
def testOutOfRangeLargeOldFormat(self):
self.assertRaises( ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999" )
def tearDown(self):
self.samfile.close()
-
class TestWrongFormat(unittest.TestCase):
'''test cases for opening files not in bam/sam format.'''
def testMate( self ):
'''test mate access.'''
- readnames = [ x.split("\t")[0] for x in open( "ex1.sam", "r" ).readlines() ]
+ readnames = [ x.split("\t")[0] for x in open( "ex1.sam", "rb" ).readlines() ]
counts = collections.defaultdict( int )
for x in readnames: counts[x] += 1
def testSort( self ):
self.assertRaises( pysam.SamtoolsError, pysam.sort, "missing_file" )
+class TestSamfileIndex( unittest.TestCase):
+
+ def testIndex( self ):
+ samfile = pysam.Samfile( "ex1.bam", "rb" )
+ index = pysam.IndexedReads( samfile )
+ index.build()
+
+ reads = collections.defaultdict( int )
+
+ for read in samfile: reads[read.qname] += 1
+
+ for qname, counts in reads.iteritems():
+ found = list(index.find( qname ))
+ self.assertEqual( len(found), counts )
+ for x in found: self.assertEqual( x.qname, qname )
+
+
if __name__ == "__main__":
# build data files
print "building data files"
def setUp( self ):
self.tabix = pysam.Tabixfile( self.filename )
- lines = gzip.open(self.filename).readlines()
+ lines = [ x for x in gzip.open(self.filename).readlines() if not x.startswith("#") ]
# creates index of contig, start, end, adds content without newline.
self.compare = [
(x[0][0], int(x[0][3]), int(x[0][4]), x[1])
# check that contigs is read-only
self.assertRaises( AttributeError, setattr, self.tabix, "contigs", ["chr1", "chr2"] )
+ def testHeader( self ):
+ ref = []
+ for x in gzip.open( self.filename ):
+ if not x.startswith("#"): break
+ ref.append( x[:-1] )
+ header = list( self.tabix.header )
+ self.assertEqual( ref, header )
+
class TestParser( unittest.TestCase ):
filename = "example.gtf.gz"
def setUp( self ):
self.tabix = pysam.Tabixfile( self.filename )
- self.compare = [ x[:-1].split("\t") for x in gzip.open( self.filename, "r") ]
-
- def testGTF( self ):
-
- for x, r in enumerate(self.tabix.fetch( parser = pysam.asGTF() )):
- self.assertEqual( "\t".join( self.compare[x]), str(r) )
+ self.compare = [ x[:-1].split("\t") for x in gzip.open( self.filename, "r") if not x.startswith("#") ]
- def testTuple( self ):
+ def testRead( self ):
for x, r in enumerate(self.tabix.fetch( parser = pysam.asTuple() )):
self.assertEqual( self.compare[x], list(r) )
-
self.assertEqual( len(self.compare[x]), len(r) )
+
for c in range(0,len(r)):
self.assertEqual( self.compare[x][c], r[c] )
+ def testWrite( self ):
+
+ for x, r in enumerate(self.tabix.fetch( parser = pysam.asTuple() )):
+ self.assertEqual( self.compare[x], list(r) )
+ c = list(r)
+ for y in range(len(r)):
+ r[y] = "test_%05i" % y
+ c[y] = "test_%05i" % y
+ self.assertEqual( c, list(r) )
+ self.assertEqual( "\t".join( c ), str(r) )
+ # check second assignment
+ for y in range(len(r)):
+ r[y] = "test_%05i" % y
+ self.assertEqual( c, list(r) )
+ self.assertEqual( "\t".join( c ), str(r) )
+
+ def testUnset( self ):
+ for x, r in enumerate(self.tabix.fetch( parser = pysam.asTuple() )):
+ self.assertEqual( self.compare[x], list(r) )
+ c = list(r)
+ e = list(r)
+ for y in range(len(r)):
+ r[y] = c[y] = None
+ e[y] = ""
+ self.assertEqual( c, list(r) )
+ self.assertEqual( "\t".join(e), str(r) )
+
+class TestGTF( TestParser ):
+ def testRead( self ):
+
+ for x, r in enumerate(self.tabix.fetch( parser = pysam.asGTF() )):
+ self.assertEqual( "\t".join( self.compare[x]), str(r) )
+
+class TestBed( unittest.TestCase ):
+ filename = "example.bed.gz"
+
+ def setUp( self ):
+
+ self.tabix = pysam.Tabixfile( self.filename )
+ self.compare = [ x[:-1].split("\t") for x in gzip.open( self.filename, "r") if not x.startswith("#") ]
+
+ def testRead( self ):
+
+ for x, r in enumerate(self.tabix.fetch( parser = pysam.asBed() )):
+ c = self.compare[x]
+ self.assertEqual( "\t".join( c ), str(r) )
+ self.assertEqual( list(c), list(r) )
+ self.assertEqual( c[0], r.contig)
+ self.assertEqual( int(c[1]), r.start)
+ self.assertEqual( int(c[2]), r.end)
+
+ def testWrite( self ):
+
+ for x, r in enumerate(self.tabix.fetch( parser = pysam.asBed() )):
+ c = self.compare[x]
+ self.assertEqual( "\t".join( c ), str(r) )
+ self.assertEqual( list(c), list(r) )
+
+ r.contig = "test"
+ self.assertEqual( "test", r.contig)
+ self.assertEqual( "test", r[0])
+
+ r.start += 1
+ self.assertEqual( int(c[1]) + 1, r.start )
+ self.assertEqual( str(int(c[1]) + 1), r[1] )
+
+ r.end += 1
+ self.assertEqual( int(c[2]) + 1, r.end )
+ self.assertEqual( str(int(c[2]) + 1), r[2] )
+
+class TestVCF( TestParser ):
+
+ filename = "example.vcf40.gz"
+ columns = ("contig", "pos", "id",
+ "ref", "alt", "qual",
+ "filter", "info", "format" )
+
+ def testRead( self ):
+
+ ncolumns = len(self.columns)
+
+ for x, r in enumerate(self.tabix.fetch( parser = pysam.asVCF() )):
+ c = self.compare[x]
+ for y, field in enumerate( self.columns ):
+ if field == "pos":
+ self.assertEqual( int(c[y])-1, getattr( r, field ) )
+ self.assertEqual( int(c[y])-1, r.pos )
+ else:
+ self.assertEqual( c[y], getattr( r, field ),
+ "mismatch in field %s: %s != %s" %\
+ ( field,c[y], getattr( r, field ) ) )
+ self.assertEqual( len(c), len( r ) + ncolumns )
+
+ for y in range(len(c) - ncolumns):
+ self.assertEqual( c[ncolumns+y], r[y] )
+
+ def testWrite( self ):
+
+ ncolumns = len(self.columns)
+
+ for x, r in enumerate(self.tabix.fetch( parser = pysam.asVCF() )):
+ c = self.compare[x]
+ for y, field in enumerate( self.columns ):
+ if field == "pos":
+ r.pos += 1
+ self.assertEqual( int(c[y]), getattr( r, field ) )
+ self.assertEqual( int(c[y]), r.pos )
+ else:
+ setattr( r, field, "test_%i" % y)
+ c[y] = "test_%i" % y
+ self.assertEqual( c[y], getattr( r, field ),
+ "mismatch in field %s: %s != %s" %\
+ ( field,c[y], getattr( r, field ) ) )
+
+ self.assertEqual( len(c), len( r ) + ncolumns )
+
+ for y in range(len(c) - ncolumns):
+ c[ncolumns+y] = "test_%i" % y
+ r[y] = "test_%i" % y
+ self.assertEqual( c[ncolumns+y], r[y] )
+
if __name__ == "__main__":
+
unittest.main()
projects / python-pysam.git / commitdiff