From: Charles Plessy Date: Fri, 9 Aug 2013 09:34:23 +0000 (+0900) Subject: Imported Upstream version 0.7.1 X-Git-Tag: archive/raspbian/0.22.0+ds-1+rpi1~1^2^2~434^2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=11d21483ba2333249960e114ca3785d4476ac3d7;p=python-pysam.git Imported Upstream version 0.7.1 --- diff --git a/MANIFEST.in b/MANIFEST.in index f613856..0fe44fe 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -21,6 +21,7 @@ include pysam/TabProxies.pxd include pysam/cvcf.pyx include pysam/cvcf.pxd include pysam/cvcf.c +include pysam/*.c include pysam/pysam_util.h include samtools/*.h include samtools/*/*.h @@ -44,6 +45,7 @@ include tests/example.py include tests/pysam_test.py include tests/segfault_tests.py include tests/example_*.sam +include tests/example_btag.bam include tests/tag_bug.bam include tests/example.vcf40 include tests/example_empty_header.bam @@ -56,4 +58,3 @@ include tests/example.gtf.gz.tbi include tests/example.bed.gz include tests/example.bed.gz.tbi include tests/vcf-examples/*.vcf - diff --git a/PKG-INFO b/PKG-INFO index 6e727bf..e0b77b4 100644 --- a/PKG-INFO +++ b/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 1.1 Name: pysam -Version: 0.7 +Version: 0.7.1 Summary: pysam Home-page: http://code.google.com/p/pysam/ Author: Andreas Heger diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO index 6e727bf..e0b77b4 100644 --- a/pysam.egg-info/PKG-INFO +++ b/pysam.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 1.1 Name: pysam -Version: 0.7 +Version: 0.7.1 Summary: pysam Home-page: http://code.google.com/p/pysam/ Author: Andreas Heger diff --git a/pysam.egg-info/SOURCES.txt b/pysam.egg-info/SOURCES.txt index b59e914..31820bd 100644 --- a/pysam.egg-info/SOURCES.txt +++ b/pysam.egg-info/SOURCES.txt @@ -10,7 +10,6 @@ pysam/Pileup.py pysam/TabProxies.c pysam/TabProxies.pxd pysam/TabProxies.pyx -pysam/VCF.py pysam/__init__.py pysam/csamtools.c pysam/csamtools.pxd @@ -141,6 +140,7 @@ tests/example.gtf.gz tests/example.gtf.gz.tbi tests/example.py tests/example.vcf40 +tests/example_btag.bam tests/example_btag.sam tests/example_empty_header.bam tests/example_unmapped_reads_no_sq.sam diff --git a/pysam/TabProxies.c b/pysam/TabProxies.c index 8c393e0..df3c35e 100644 --- a/pysam/TabProxies.c +++ b/pysam/TabProxies.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.16 on Tue Nov 20 16:56:59 2012 */ +/* Generated by Cython 0.16 on Tue Nov 20 15:06:33 2012 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -970,7 +970,7 @@ static char __pyx_k_54[] = "feature strand."; static char __pyx_k_55[] = "feature frame."; static char __pyx_k_56[] = "feature attributes (as a string)."; static char __pyx_k_57[] = "getfilesystemencoding"; -static char __pyx_k_60[] = "/ifs/devel/pysam/pysam/TabProxies.pyx"; +static char __pyx_k_60[] = "/home/andreas/devel/pysam/pysam/TabProxies.pyx"; static char __pyx_k__v[] = "v"; static char __pyx_k__id[] = "id"; static char __pyx_k__alt[] = "alt"; diff --git a/pysam/VCF.py b/pysam/VCF.py deleted file mode 100644 index 94d63f8..0000000 --- a/pysam/VCF.py +++ /dev/null @@ -1,1087 +0,0 @@ -# -# 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'] = '' - 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": - self._version = 41 - 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 and D - 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 not in [33,40,41]: raise ValueError("Can only handle v3.3, v4.0 and v4.1 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 and D - 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 - - - - diff --git a/pysam/__init__.py b/pysam/__init__.py index f4f1138..7c001d1 100644 --- a/pysam/__init__.py +++ b/pysam/__init__.py @@ -113,7 +113,7 @@ SAMTOOLS_DISPATCH = { } # instantiate samtools commands as python functions -for key, options in SAMTOOLS_DISPATCH.iteritems(): +for key, options in SAMTOOLS_DISPATCH.items(): cmd, parser = options globals()[key] = SamtoolsDispatcher(cmd, parser) diff --git a/pysam/csamtools.c b/pysam/csamtools.c index b7495db..35b4522 100644 --- a/pysam/csamtools.c +++ b/pysam/csamtools.c @@ -1,12 +1,11 @@ -/* Generated by Cython 0.16 on Thu Nov 22 15:20:54 2012 */ +/* Generated by Cython 0.15.1 on Mon Jan 14 23:52:53 2013 */ #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. -#elif PY_VERSION_HEX < 0x02040000 - #error Cython requires Python 2.4+. #else + #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -35,22 +34,10 @@ #define PY_LONG_LONG LONG_LONG #endif -#ifndef Py_HUGE_VAL - #define Py_HUGE_VAL HUGE_VAL -#endif - -#ifdef PYPY_VERSION -#define CYTHON_COMPILING_IN_PYPY 1 -#define CYTHON_COMPILING_IN_CPYTHON 0 -#else -#define CYTHON_COMPILING_IN_PYPY 0 -#define CYTHON_COMPILING_IN_CPYTHON 1 -#endif - -#if CYTHON_COMPILING_IN_PYPY - #define __Pyx_PyCFunction_Call PyObject_Call -#else - #define __Pyx_PyCFunction_Call PyCFunction_Call +#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 @@ -63,9 +50,6 @@ #define PyNumber_Index(o) PyNumber_Int(o) #define PyIndex_Check(o) PyNumber_Check(o) #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) - #define __PYX_BUILD_PY_SSIZE_T "i" -#else - #define __PYX_BUILD_PY_SSIZE_T "n" #endif #if PY_VERSION_HEX < 0x02060000 @@ -99,25 +83,13 @@ #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) - #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) - #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) - typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); - typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ - PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ - PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) -#endif - -#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 - #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 @@ -129,17 +101,6 @@ #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif - -#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH) - #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) -#else - #define CYTHON_PEP393_ENABLED 0 - #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) - #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) -#endif - #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject @@ -207,6 +168,15 @@ #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #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) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) @@ -248,14 +218,6 @@ #define __Pyx_DOCSTR(n) (n) #endif -#if PY_MAJOR_VERSION >= 3 - #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) -#else - #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) - #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) -#endif - #ifndef __PYX_EXTERN_C #ifdef __cplusplus #define __PYX_EXTERN_C extern "C" @@ -313,7 +275,7 @@ # else # define CYTHON_UNUSED # endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# elif defined(__ICC) || defined(__INTEL_COMPILER) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED @@ -338,7 +300,7 @@ 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)) -#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) + #ifdef __GNUC__ /* Test for GCC > 2.95 */ @@ -370,7 +332,15 @@ static const char *__pyx_f[] = { "complex.pxd", }; +static PyObject *__Pyx_Generator_Next(PyObject *self); +static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); +static PyObject *__Pyx_Generator_Close(PyObject *self); +static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args, CYTHON_UNUSED PyObject *kwds); + +typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); + /*--- Type declarations ---*/ +struct __pyx_Generator_object; struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr; struct __pyx_obj_9csamtools_IteratorRow; struct __pyx_obj_9csamtools_IteratorRowAllRefs; @@ -442,8 +412,18 @@ struct __pyx_t_9csamtools_MateData { * else: * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) */ -struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr { +struct __pyx_Generator_object { PyObject_HEAD + __pyx_generator_body_t body; + int is_running; + int resume_label; + PyObject *exc_type; + PyObject *exc_value; + PyObject *exc_traceback; +}; + +struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr { + struct __pyx_Generator_object __pyx_base; PyObject *__pyx_v_x; PyObject *__pyx_v_y; PyObject *__pyx_t_0; @@ -621,7 +601,7 @@ struct __pyx_obj_9csamtools_IteratorRowRegion { * */ struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr { - PyObject_HEAD + struct __pyx_Generator_object __pyx_base; PyObject *__pyx_v_x; PyObject *__pyx_v_y; PyObject *__pyx_t_0; @@ -844,9 +824,11 @@ struct __pyx_vtabstruct_9csamtools_IteratorRowAll { int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *); }; static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll; + #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif + #if CYTHON_REFNANNY typedef struct { void (*INCREF)(void*, PyObject*, int); @@ -859,21 +841,8 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/ #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; -#ifdef WITH_THREAD - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ - if (acquire_gil) { \ - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ - PyGILState_Release(__pyx_gilstate_save); \ - } else { \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ - } -#else - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) -#endif - #define __Pyx_RefNannyFinishContext() \ - __Pyx_RefNanny->FinishContext(&__pyx_refnanny) + #define __Pyx_RefNannySetupContext(name) __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__) @@ -884,7 +853,7 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0) #else #define __Pyx_RefNannyDeclarations - #define __Pyx_RefNannySetupContext(name, acquire_gil) + #define __Pyx_RefNannySetupContext(name) #define __Pyx_RefNannyFinishContext() #define __Pyx_INCREF(r) Py_INCREF(r) #define __Pyx_DECREF(r) Py_DECREF(r) @@ -895,21 +864,23 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) #endif /* CYTHON_REFNANNY */ -#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) -#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ #ifndef CYTHON_PROFILE #define CYTHON_PROFILE 1 #endif + #ifndef CYTHON_PROFILE_REUSE_FRAME #define CYTHON_PROFILE_REUSE_FRAME 0 #endif + #if CYTHON_PROFILE + #include "compile.h" #include "frameobject.h" #include "traceback.h" + #if CYTHON_PROFILE_REUSE_FRAME #define CYTHON_FRAME_MODIFIER static #define CYTHON_FRAME_DEL @@ -917,14 +888,17 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ #define CYTHON_FRAME_MODIFIER #define CYTHON_FRAME_DEL Py_DECREF(__pyx_frame) #endif + #define __Pyx_TraceDeclarations \ static PyCodeObject *__pyx_frame_code = NULL; \ CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \ int __Pyx_use_tracing = 0; + #define __Pyx_TraceCall(funcname, srcfile, firstlineno) \ if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \ __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno); \ } + #define __Pyx_TraceException() \ if (unlikely(__Pyx_use_tracing( && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \ PyObject *exc_info = __Pyx_GetExceptionTuple(); \ @@ -934,19 +908,24 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ Py_DECREF(exc_info); \ } \ } + #define __Pyx_TraceReturn(result) \ if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \ PyThreadState_GET()->c_profilefunc( \ PyThreadState_GET()->c_profileobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \ CYTHON_FRAME_DEL; \ } + static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/ static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno); /*proto*/ + #else + #define __Pyx_TraceDeclarations #define __Pyx_TraceCall(funcname, srcfile, firstlineno) #define __Pyx_TraceException() #define __Pyx_TraceReturn(result) + #endif /* CYTHON_PROFILE */ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ @@ -963,13 +942,13 @@ static CYTHON_INLINE PyObject* __Pyx_tp_new(PyObject* type_obj) { static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ -static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/ +static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, + const char* function_name, int kw_allowed); /*proto*/ -static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/ +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, PyObject* kw_name); /*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 int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_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*/ @@ -979,6 +958,7 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ + static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; if (!j) return NULL; @@ -986,9 +966,12 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* 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)))) { @@ -1004,9 +987,11 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_ } 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)))) { @@ -1022,33 +1007,29 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize } 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) { - if (PyList_CheckExact(o)) { - Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); - if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { - PyObject *r = PyList_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } + 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)) { - Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); - if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { - PyObject *r = PyTuple_GET_ITEM(o, n); - Py_INCREF(r); - return r; - } + else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); } - else if (likely(i >= 0)) { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_item)) { - return m->sq_item(o, i); - } + else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) { + r = PySequence_GetItem(o, i); } - return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); + else { + r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); + } + return r; } static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { @@ -1073,8 +1054,8 @@ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ -static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) { - return unlikely(b < 0) ? b : !b; +static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) { + return unlikely(b < 0) ? b : !b; } static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b); @@ -1114,6 +1095,7 @@ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObjec Py_INCREF(value); #else if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) { + /* these presumably have safe hash functions */ value = PyDict_GetItem(d, key); if (unlikely(!value)) { value = default_value; @@ -1124,7 +1106,7 @@ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObjec m = __Pyx_GetAttrString(d, "get"); if (!m) return NULL; value = PyObject_CallFunctionObjArgs(m, key, - (default_value == Py_None) ? NULL : default_value, NULL); + (default_value == Py_None) ? NULL : default_value, NULL); Py_DECREF(m); } #endif @@ -1140,6 +1122,7 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); #define __Pyx_DelItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_DelItemInt_Fast(o, i) : \ __Pyx_DelItem_Generic(o, to_py_func(i))) + static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) { int r; if (!j) return -1; @@ -1147,14 +1130,14 @@ static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) { Py_DECREF(j); return r; } + static CYTHON_INLINE int __Pyx_DelItemInt_Fast(PyObject *o, Py_ssize_t i) { - if (likely(i >= 0)) { - PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; - if (likely(m && m->sq_ass_item)) { - return m->sq_ass_item(o, i, (PyObject *)NULL); - } + if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && likely(i >= 0)) + return PySequence_DelItem(o, i); + else { + PyObject *j = PyInt_FromSsize_t(i); + return __Pyx_DelItem_Generic(o, j); } - return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i)); } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ @@ -1167,47 +1150,19 @@ static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *modname); /*proto*/ -#define __Pyx_CyFunction_USED 1 -#include -#define __Pyx_CYFUNCTION_STATICMETHOD 0x01 -#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 -#define __Pyx_CYFUNCTION_CCLASS 0x04 -#define __Pyx_CyFunction_GetClosure(f) \ - (((__pyx_CyFunctionObject *) (f))->func_closure) -#define __Pyx_CyFunction_GetClassObj(f) \ - (((__pyx_CyFunctionObject *) (f))->func_classobj) -#define __Pyx_CyFunction_Defaults(type, f) \ - ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) -#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \ - ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) +#define __pyx_binding_PyCFunctionType_USED 1 + typedef struct { PyCFunctionObject func; - int flags; - PyObject *func_dict; - PyObject *func_weakreflist; - PyObject *func_name; - PyObject *func_doc; - PyObject *func_code; - PyObject *func_closure; - PyObject *func_classobj; /* No-args super() class cell */ - void *defaults; - int defaults_pyobjects; - PyObject *defaults_tuple; /* Const defaults tuple */ - PyObject *(*defaults_getter)(PyObject *); -} __pyx_CyFunctionObject; -static PyTypeObject *__pyx_CyFunctionType = 0; -#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \ - __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code) -static PyObject *__Pyx_CyFunction_New(PyTypeObject *, - PyMethodDef *ml, int flags, - PyObject *self, PyObject *module, - PyObject* code); -static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, - size_t size, - int pyobjects); -static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, - PyObject *tuple); -static int __Pyx_CyFunction_init(void); +} __pyx_binding_PyCFunctionType_object; + +static PyTypeObject __pyx_binding_PyCFunctionType_type; +static PyTypeObject *__pyx_binding_PyCFunctionType = NULL; + +static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */ +#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL) + +static int __pyx_binding_PyCFunctionType_init(void); /* proto */ static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ @@ -1277,25 +1232,6 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject * static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ -#define __Pyx_Generator_USED -#include -typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); -typedef struct { - PyObject_HEAD - __pyx_generator_body_t body; - PyObject *closure; - int is_running; - int resume_label; - PyObject *exc_type; - PyObject *exc_value; - PyObject *exc_traceback; - PyObject *gi_weakreflist; - PyObject *classobj; -} __pyx_GeneratorObject; -static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, - PyObject *closure); -static int __pyx_Generator_init(void); - static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename); /*proto*/ @@ -1303,38 +1239,15 @@ static int __Pyx_check_binary_version(void); static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ -#if !defined(__Pyx_PyIdentifier_FromString) -#if PY_MAJOR_VERSION < 3 - #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) -#else - #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) -#endif -#endif - static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ -typedef struct { - int code_line; - PyCodeObject* code_object; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); - -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); /*proto*/ +static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno, + int __pyx_lineno, const char *__pyx_filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ - /* Module declarations from 'cpython.version' */ /* Module declarations from 'cpython.ref' */ @@ -1429,6 +1342,7 @@ static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0; static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0; static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0; static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0; +static PyTypeObject *__pyx_ptype_9csamtools___pyx_Generator = 0; static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct__genexpr = 0; static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = 0; static PyObject *__pyx_v_9csamtools__FILENAME_ENCODING = 0; @@ -1480,191 +1394,6 @@ static PyObject *__pyx_builtin_max; static PyObject *__pyx_builtin_chr; static PyObject *__pyx_builtin_open; static PyObject *__pyx_builtin_UnicodeDecodeError; -static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */ -static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ -static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen); /* proto */ -static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */ -static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */ -static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */ -static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile); /* proto */ -static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */ -static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */ -static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */ -static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */ -static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ -static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ -static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ -static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static void __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_other); /* proto */ -static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */ -static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */ -static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */ -static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */ -static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */ -static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */ -static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */ static char __pyx_k_1[] = "Argument must be string or unicode."; static char __pyx_k_3[] = "Argument must be string, bytes or unicode."; static char __pyx_k_5[] = "\t"; @@ -1722,7 +1451,6 @@ static char __pyx_k__H[] = "H"; static char __pyx_k__I[] = "I"; static char __pyx_k__S[] = "S"; static char __pyx_k__Z[] = "Z"; -static char __pyx_k__a[] = "a"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__d[] = "d"; @@ -1854,11 +1582,10 @@ static char __pyx_k_249[] = "getfilesystemencoding"; static char __pyx_k_250[] = "MIDNSHP=X"; static char __pyx_k_251[] = "([MIDNSHP=X])(\\d+)"; static char __pyx_k_253[] = "=ACMGRSVTWYHKDBN"; -static char __pyx_k_256[] = "/ifs/devel/pysam/pysam/csamtools.pyx"; -static char __pyx_k_257[] = "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_266[] = "\n stderr is captured.\n "; -static char __pyx_k_273[] = "does nothing. stderr can't be redirected on windows"; -static char __pyx_k_290[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html"; +static char __pyx_k_254[] = "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_255[] = "\n stderr is captured.\n "; +static char __pyx_k_256[] = "does nothing. stderr can't be redirected on windows"; +static char __pyx_k_262[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html"; static char __pyx_k__AS[] = "AS"; static char __pyx_k__CL[] = "CL"; static char __pyx_k__CN[] = "CN"; @@ -1877,6 +1604,7 @@ static char __pyx_k__PG[] = "PG"; static char __pyx_k__PI[] = "PI"; static char __pyx_k__PL[] = "PL"; static char __pyx_k__PN[] = "PN"; +static char __pyx_k__PP[] = "PP"; static char __pyx_k__PU[] = "PU"; static char __pyx_k__RG[] = "RG"; static char __pyx_k__SM[] = "SM"; @@ -1900,11 +1628,9 @@ static char __pyx_k__bin[] = "bin"; static char __pyx_k__chr[] = "chr"; static char __pyx_k__dup[] = "dup"; static char __pyx_k__end[] = "end"; -static char __pyx_k__inf[] = "inf"; static char __pyx_k__map[] = "map"; static char __pyx_k__max[] = "max"; static char __pyx_k__min[] = "min"; -static char __pyx_k__ofd[] = "ofd"; static char __pyx_k__ord[] = "ord"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__raw[] = "raw"; @@ -1949,7 +1675,6 @@ static char __pyx_k__warn[] = "warn"; static char __pyx_k___open[] = "_open"; static char __pyx_k__ascii[] = "ascii"; static char __pyx_k__bqual[] = "bqual"; -static char __pyx_k__cargs[] = "cargs"; static char __pyx_k__cigar[] = "cigar"; static char __pyx_k__close[] = "close"; static char __pyx_k__flush[] = "flush"; @@ -1987,7 +1712,6 @@ static char __pyx_k__record[] = "record"; static char __pyx_k__region[] = "region"; static char __pyx_k__remove[] = "remove"; static char __pyx_k__reopen[] = "reopen"; -static char __pyx_k__retval[] = "retval"; static char __pyx_k__sorted[] = "sorted"; static char __pyx_k__stderr[] = "stderr"; static char __pyx_k__stdout[] = "stdout"; @@ -2037,10 +1761,6 @@ static char __pyx_k__genotype[] = "genotype"; static char __pyx_k__nextiter[] = "nextiter"; static char __pyx_k__platform[] = "platform"; 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__stdout_f[] = "stdout_f"; -static char __pyx_k__stdout_h[] = "stdout_h"; static char __pyx_k__tempfile[] = "tempfile"; static char __pyx_k__template[] = "template"; static char __pyx_k__truncate[] = "truncate"; @@ -2068,8 +1788,6 @@ static char __pyx_k__IS_PYTHON3[] = "IS_PYTHON3"; static char __pyx_k__PileupRead[] = "PileupRead"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k___buildLine[] = "_buildLine"; -static char __pyx_k__out_stderr[] = "out_stderr"; -static char __pyx_k__out_stdout[] = "out_stdout"; static char __pyx_k__references[] = "references"; static char __pyx_k__startswith[] = "startswith"; static char __pyx_k__AlignedRead[] = "AlignedRead"; @@ -2082,7 +1800,6 @@ static char __pyx_k__collections[] = "collections"; static char __pyx_k__defaultdict[] = "defaultdict"; static char __pyx_k__nreferences[] = "nreferences"; static char __pyx_k__snp_quality[] = "snp_quality"; -static char __pyx_k__stdout_save[] = "stdout_save"; static char __pyx_k__IndexedReads[] = "IndexedReads"; static char __pyx_k__PileupColumn[] = "PileupColumn"; static char __pyx_k___parseRegion[] = "_parseRegion"; @@ -2175,12 +1892,11 @@ static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_24; static PyObject *__pyx_n_s_249; static PyObject *__pyx_kp_s_251; +static PyObject *__pyx_kp_s_254; +static PyObject *__pyx_kp_s_255; static PyObject *__pyx_kp_s_256; -static PyObject *__pyx_kp_s_257; -static PyObject *__pyx_kp_s_266; -static PyObject *__pyx_kp_s_273; +static PyObject *__pyx_kp_s_262; static PyObject *__pyx_kp_s_29; -static PyObject *__pyx_kp_s_290; static PyObject *__pyx_kp_u_3; static PyObject *__pyx_kp_s_30; static PyObject *__pyx_kp_s_31; @@ -2266,6 +1982,7 @@ static PyObject *__pyx_n_s__PG; static PyObject *__pyx_n_s__PI; static PyObject *__pyx_n_s__PL; static PyObject *__pyx_n_s__PN; +static PyObject *__pyx_n_s__PP; static PyObject *__pyx_n_s__PU; static PyObject *__pyx_n_s__PileupColumn; static PyObject *__pyx_n_s__PileupProxy; @@ -2308,7 +2025,6 @@ static PyObject *__pyx_n_s___isOpen; static PyObject *__pyx_n_s___open; static PyObject *__pyx_n_s___parseRegion; static PyObject *__pyx_n_s___samtools_dispatch; -static PyObject *__pyx_n_s__a; static PyObject *__pyx_n_s__add_sq_text; static PyObject *__pyx_n_s__alignment; static PyObject *__pyx_n_s__all; @@ -2321,7 +2037,6 @@ static PyObject *__pyx_n_s__bqual; static PyObject *__pyx_n_s__c; static PyObject *__pyx_n_s__calcsize; static PyObject *__pyx_n_s__callback; -static PyObject *__pyx_n_s__cargs; static PyObject *__pyx_n_s__catch_stdout; static PyObject *__pyx_n_s__check_header; static PyObject *__pyx_n_s__check_sq; @@ -2365,7 +2080,6 @@ static PyObject *__pyx_n_s__i; static PyObject *__pyx_n_s__id; static PyObject *__pyx_n_s__indel; static PyObject *__pyx_n_s__index; -static PyObject *__pyx_n_s__inf; static PyObject *__pyx_n_s__is_del; static PyObject *__pyx_n_s__is_head; static PyObject *__pyx_n_s__is_tail; @@ -2399,13 +2113,10 @@ static PyObject *__pyx_n_s__n_cigar; static PyObject *__pyx_n_s__nextiter; static PyObject *__pyx_n_s__nreferences; static PyObject *__pyx_n_s__object; -static PyObject *__pyx_n_s__ofd; static PyObject *__pyx_n_s__offset; static PyObject *__pyx_n_s__open; static PyObject *__pyx_n_s__ord; static PyObject *__pyx_n_s__os; -static PyObject *__pyx_n_s__out_stderr; -static PyObject *__pyx_n_s__out_stdout; static PyObject *__pyx_n_s__pack_into; static PyObject *__pyx_n_s__path; static PyObject *__pyx_n_s__pileups; @@ -2438,7 +2149,6 @@ static PyObject *__pyx_n_s__release; static PyObject *__pyx_n_s__remove; static PyObject *__pyx_n_s__reopen; static PyObject *__pyx_n_s__restore; -static PyObject *__pyx_n_s__retval; static PyObject *__pyx_n_s__rlen; static PyObject *__pyx_n_s__rname; static PyObject *__pyx_n_s__s; 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-static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */ +static PyObject *__pyx_k_tuple_261; +static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */ /* "csamtools.pyx":140 * cdef char* CODE2CIGAR= "MIDNSHP=X" @@ -2638,15 +2314,14 @@ static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_gen * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) */ -static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self) { +static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_9csamtools_1genexpr[] = "genexpr()"; +static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) { struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope; 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_1 = __Pyx_PyInt_to_py_int16_t((((int16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -4082,6 +3753,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) { * s += 2 * elif auxtype == 'i': */ + if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_1 = __Pyx_PyInt_to_py_uint16_t((((uint16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_1 = PyFloat_FromDouble((((float *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -4245,7 +3928,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) { __pyx_t_5 = __Pyx_PyInt_to_py_int32_t(__pyx_v_nvalues); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); 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/*proto*/ +static char __pyx_doc_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)"; +static PyMethodDef __pyx_mdef_9csamtools_12PileupColumn___str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pf_9csamtools_12PileupColumn___str__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12PileupColumn___str__)}; +static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -4373,8 +4045,9 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__str__", 0); + __Pyx_RefNannySetupContext("__str__"); __Pyx_TraceCall("__str__", __pyx_f[0], 260); + __pyx_self = __pyx_self; /* "csamtools.pyx":261 * ''' @@ -4409,7 +4082,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); 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/*proto*/ +static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self) { Py_ssize_t __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -5226,7 +4797,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__len__", 0); + __Pyx_RefNannySetupContext("__len__"); __Pyx_TraceCall("__len__", __pyx_f[0], 396); /* "csamtools.pyx":397 @@ -5236,7 +4807,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam * raise ValueError( "calling len() on closed file" ) * */ - __pyx_t_1 = (__pyx_v_self->fastafile == NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL); if (__pyx_t_1) { /* "csamtools.pyx":398 @@ -5251,9 +4822,9 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":400 * raise ValueError( "calling len() on closed file" ) @@ -5262,7 +4833,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam * * def _open( self, */ - __pyx_r = faidx_fetch_nseq(__pyx_v_self->fastafile); + __pyx_r = faidx_fetch_nseq(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile); goto __pyx_L0; __pyx_r = 0; @@ -5277,18 +4848,6 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/ -static char __pyx_doc_9csamtools_9Fastafile_6_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n "; -static PyObject *__pyx_pw_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) { - PyObject *__pyx_r = 0; 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":411 * # close a previously opened file @@ -5338,12 +4899,12 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo * filename = _my_encodeFilename(filename) * self._filename = strdup(filename) */ - __pyx_t_1 = (__pyx_v_self->_filename != NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL); if (__pyx_t_1) { - free(__pyx_v_self->_filename); - goto __pyx_L4; + free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename); 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__Pyx_GIVEREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; @@ -5408,9 +4969,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + goto __pyx_L7; } - __pyx_L5:; + __pyx_L7:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -5427,18 +4988,6 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_9csamtools_9Fastafile_8close[] = "Fastafile.close(self)"; -static PyObject *__pyx_pw_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("close (wrapper)", 0); 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/* "csamtools.pyx":420 @@ -5462,7 +5013,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo * fai_destroy( self.fastafile ) * self.fastafile = NULL */ - __pyx_t_1 = (__pyx_v_self->fastafile != NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL); if (__pyx_t_1) { /* "csamtools.pyx":421 @@ -5472,7 +5023,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo * self.fastafile = NULL * */ - fai_destroy(__pyx_v_self->fastafile); + fai_destroy(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile); /* "csamtools.pyx":422 * if self.fastafile != NULL: @@ -5481,10 +5032,10 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo * * def __dealloc__(self): */ - __pyx_v_self->fastafile = NULL; - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); __Pyx_XGIVEREF(__pyx_r); @@ -5493,15 +5044,6 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo return __pyx_r; } -/* Python wrapper */ -static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self) { - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_9csamtools_9Fastafile_10__dealloc__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); -} - /* "csamtools.pyx":424 * self.fastafile = NULL * @@ -5510,7 +5052,8 @@ static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self) * if self._filename != NULL: free(self._filename) */ -static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) { +static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; @@ -5519,7 +5062,7 @@ static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamt const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__dealloc__", 0); + __Pyx_RefNannySetupContext("__dealloc__"); __Pyx_TraceCall("__dealloc__", __pyx_f[0], 424); /* "csamtools.pyx":425 @@ -5529,7 +5072,7 @@ static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamt * if self._filename != NULL: free(self._filename) * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); 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- __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_9Fastafile_8filename___get__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":430 * property filename: * '''number of :term:`filename` associated with this object.''' @@ -5579,7 +5111,8 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_8filename_1__get__(PyObject *__p * return self._filename */ -static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -5590,7 +5123,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 430); /* "csamtools.pyx":431 @@ -5600,7 +5133,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o * return self._filename * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -5614,9 +5147,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":432 * def __get__(self): @@ -5626,7 +5159,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o * def fetch( self, */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; @@ -5646,18 +5179,38 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o return __pyx_r; 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Similarly, if *end* is None, the sequence\n until the last base is returned.\n\n Alternatively, a samtools :term:`region` string can be supplied.\n "; +static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_region = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0}; - PyObject *__pyx_r = 0; + int __pyx_v_length; + char *__pyx_v_seq; + PyObject *__pyx_v_py_seq = NULL; + PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("fetch (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + char *__pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("fetch"); + __Pyx_TraceCall("fetch", __pyx_f[0], 434); { PyObject* values[4] = {0,0,0,0}; @@ -5698,8 +5251,7 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, values[3] = ((PyObject *)Py_None); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); @@ -5708,7 +5260,7 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference); @@ -5731,7 +5283,7 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -5756,36 +5308,6 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_9csamtools_9Fastafile_12fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "csamtools.pyx":434 - * return self._filename - * - * def fetch( self, # <<<<<<<<<<<<<< - * reference = None, - * start = None, - */ - -static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) { - int __pyx_v_length; - char *__pyx_v_seq; - PyObject *__pyx_v_py_seq = NULL; - PyObject *__pyx_r = NULL; - __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; - PyObject *__pyx_t_2 = NULL; - int __pyx_t_3; - int __pyx_t_4; - char *__pyx_t_5; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("fetch", 0); - __Pyx_TraceCall("fetch", __pyx_f[0], 434); __Pyx_INCREF(__pyx_v_start); __Pyx_INCREF(__pyx_v_end); __Pyx_INCREF(__pyx_v_region); @@ -5797,7 +5319,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto * raise ValueError( "I/O operation on closed file" ) * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -5819,9 +5341,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":461 * cdef char * seq @@ -5848,9 +5370,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + goto __pyx_L8; } - __pyx_L5:; + __pyx_L8:; /* "csamtools.pyx":463 * if not region: @@ -5864,9 +5386,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_INCREF(__pyx_int_0); __Pyx_DECREF(__pyx_v_start); __pyx_v_start = __pyx_int_0; - goto __pyx_L6; + goto __pyx_L9; } - __pyx_L6:; + __pyx_L9:; /* "csamtools.pyx":464 * if reference is None: raise ValueError( 'no sequence/region supplied.' ) @@ -5882,9 +5404,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_DECREF(__pyx_v_end); __pyx_v_end = __pyx_t_2; __pyx_t_2 = 0; - goto __pyx_L7; + goto __pyx_L10; } - __pyx_L7:; + __pyx_L10:; /* "csamtools.pyx":466 * if end is None: end = max_pos -1 @@ -5899,7 +5421,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (__pyx_t_3) { __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_INCREF(__pyx_v_start); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_start); __Pyx_GIVEREF(__pyx_v_start); @@ -5910,7 +5432,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -5920,9 +5442,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L8; + goto __pyx_L11; } - __pyx_L8:; + __pyx_L11:; /* "csamtools.pyx":467 * @@ -5940,9 +5462,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_INCREF(((PyObject *)__pyx_kp_b_16)); __pyx_r = ((PyObject *)__pyx_kp_b_16); goto __pyx_L0; - goto __pyx_L9; + goto __pyx_L12; } - __pyx_L9:; + __pyx_L12:; /* "csamtools.pyx":469 * if start == end: return b"" @@ -5968,7 +5490,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -5978,9 +5500,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L10; + goto __pyx_L13; } - __pyx_L10:; + __pyx_L13:; /* "csamtools.pyx":470 * # valid ranges are from 0 to 2^29-1 @@ -6006,7 +5528,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -6016,9 +5538,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L11; + goto __pyx_L14; } - __pyx_L11:; + __pyx_L14:; /* "csamtools.pyx":479 * # end-1, @@ -6030,7 +5552,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __pyx_t_1 = PyNumber_Add(__pyx_v_start, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_INCREF(__pyx_v_reference); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference); __Pyx_GIVEREF(__pyx_v_reference); @@ -6072,9 +5594,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_DECREF(__pyx_v_region); __pyx_v_region = __pyx_t_2; __pyx_t_2 = 0; - goto __pyx_L12; + goto __pyx_L15; } - __pyx_L12:; + __pyx_L15:; /* "csamtools.pyx":483 * region = region.encode('ascii') @@ -6092,8 +5614,8 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto * else: * # samtools adds a '\0' at the end */ - __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length)); - goto __pyx_L4; + __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length)); + goto __pyx_L7; } /*else*/ { @@ -6105,9 +5627,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto * # copy to python */ __pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length)); + __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length)); } - __pyx_L4:; + __pyx_L7:; /* "csamtools.pyx":490 * @@ -6130,7 +5652,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto __Pyx_INCREF(((PyObject *)__pyx_kp_b_16)); __pyx_r = ((PyObject *)__pyx_kp_b_16); goto __pyx_L0; - goto __pyx_L13; + goto __pyx_L16; } /*else*/ { @@ -6150,7 +5672,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto * finally: * free(seq) */ - __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L15;} + __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; 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__Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("_fetch", 0); + __Pyx_RefNannySetupContext("_fetch"); __Pyx_TraceCall("_fetch", __pyx_f[0], 500); /* "csamtools.pyx":507 @@ -6263,13 +5785,13 @@ static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fa * ''' */ -static int __pyx_f_9csamtools_count_callback(CYTHON_UNUSED bam1_t *__pyx_v_alignment, void *__pyx_v_f) { +static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) { int *__pyx_v_counter; int __pyx_r; __Pyx_RefNannyDeclarations long __pyx_t_1; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("count_callback", 0); + __Pyx_RefNannySetupContext("count_callback"); __Pyx_TraceCall("count_callback", __pyx_f[0], 512); /* "csamtools.pyx":515 @@ -6313,7 +5835,7 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p int __pyx_t_2; int __pyx_t_3; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("mate_callback", 0); + __Pyx_RefNannySetupContext("mate_callback"); 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int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("_isOpen", 0); + __Pyx_RefNannySetupContext("_isOpen"); __Pyx_TraceCall("_isOpen", __pyx_f[0], 602); /* "csamtools.pyx":604 @@ -6542,7 +6039,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtoo * def _hasIndex( self ): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -6561,18 +6058,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtoo return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); 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__Pyx_INCREF(__pyx_v_filename); __Pyx_INCREF(__pyx_v_referencenames); __Pyx_INCREF(__pyx_v_text); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":630 * @@ -6913,19 +6385,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * referencenames=referencenames, * referencelengths=referencelengths, */ - __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __Pyx_INCREF(__pyx_v_filename); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_filename); __Pyx_GIVEREF(__pyx_v_filename); __Pyx_INCREF(((PyObject *)__pyx_n_s__rb)); PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb)); - __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_7)); - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} /* "csamtools.pyx":633 * try: @@ -6934,7 +6406,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * referencelengths=referencelengths, * text=text, header=header, port=port, */ - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} /* "csamtools.pyx":634 * self._open(filename, 'rb', template=template, @@ -6943,7 +6415,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * text=text, header=header, port=port, * check_header=check_header, */ - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} /* "csamtools.pyx":635 * referencenames=referencenames, @@ -6952,9 +6424,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * check_header=check_header, * check_sq=check_sq) */ - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} /* "csamtools.pyx":636 * referencelengths=referencelengths, @@ -6963,7 +6435,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * check_sq=check_sq) * return */ - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} /* "csamtools.pyx":637 * text=text, header=header, port=port, @@ -6972,8 +6444,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * return * except ValueError, msg: */ - if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} - __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} + __pyx_t_8 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; @@ -6989,19 +6461,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools */ __Pyx_XDECREF(__pyx_r); __pyx_r = Py_None; __Pyx_INCREF(Py_None); - goto __pyx_L8_try_return; + goto __pyx_L11_try_return; } __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; - goto __pyx_L11_try_end; - __pyx_L8_try_return:; + goto __pyx_L14_try_end; + __pyx_L11_try_return:; __Pyx_XGIVEREF(__pyx_t_2); __Pyx_XGIVEREF(__pyx_t_3); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4); goto __pyx_L0; - __pyx_L4_error:; + __pyx_L7_error:; __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; @@ -7017,7 +6489,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_9 = PyErr_ExceptionMatches(__pyx_builtin_ValueError); if (__pyx_t_9) { __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} + if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_GOTREF(__pyx_t_7); __Pyx_GOTREF(__pyx_t_6); @@ -7026,20 +6498,20 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - goto __pyx_L5_exception_handled; + goto __pyx_L8_exception_handled; } - __pyx_L6_except_error:; + __pyx_L9_except_error:; __Pyx_XGIVEREF(__pyx_t_2); __Pyx_XGIVEREF(__pyx_t_3); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4); goto __pyx_L1_error; - __pyx_L5_exception_handled:; + __pyx_L8_exception_handled:; __Pyx_XGIVEREF(__pyx_t_2); __Pyx_XGIVEREF(__pyx_t_3); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4); - __pyx_L11_try_end:; + __pyx_L14_try_end:; } /* "csamtools.pyx":642 @@ -7049,10 +6521,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * referencenames=referencenames, * referencelengths=referencelengths, */ - __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_INCREF(__pyx_v_filename); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename); __Pyx_GIVEREF(__pyx_v_filename); @@ -7109,7 +6581,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * */ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_5 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; @@ -7126,9 +6598,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_XDECREF(__pyx_r); __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":650 * return @@ -7194,17 +6666,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * self.samfile = NULL * */ - __pyx_t_1 = (__pyx_v_self->samfile != NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL); if (__pyx_t_1) { - __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - goto __pyx_L14; + goto __pyx_L17; } - __pyx_L14:; + __pyx_L17:; /* "csamtools.pyx":656 * # close a previously opened file @@ -7213,7 +6685,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * * cdef bam_header_t * header_to_write */ - __pyx_v_self->samfile = NULL; + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL; /* "csamtools.pyx":659 * @@ -7231,12 +6703,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * filename = _my_encodeFilename(filename) * cdef bytes bmode = mode.encode('ascii') */ - __pyx_t_1 = (__pyx_v_self->_filename != NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL); if (__pyx_t_1) { - free(__pyx_v_self->_filename); - goto __pyx_L15; + free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename); + goto __pyx_L18; } - __pyx_L15:; + __pyx_L18:; /* "csamtools.pyx":662 * @@ -7275,7 +6747,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * */ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_filename = strdup(__pyx_t_12); + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = strdup(__pyx_t_12); /* "csamtools.pyx":667 * #cfilename = filename.encode(_FILENAME_ENCODING) @@ -7285,7 +6757,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * self.isbam = len(mode) > 1 and mode[1] == 'b' */ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0); + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0); /* "csamtools.pyx":669 * self.isstream = strcmp( filename, "-" ) == 0 @@ -7305,7 +6777,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools } else { __pyx_t_11 = __pyx_t_1; } - __pyx_v_self->isbam = __pyx_t_11; + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = __pyx_t_11; /* "csamtools.pyx":671 * self.isbam = len(mode) > 1 and mode[1] == 'b' @@ -7339,7 +6811,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * strncmp(filename,"ftp:",4) == 0 * */ - __pyx_v_self->isremote = __pyx_t_10; + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote = __pyx_t_10; /* "csamtools.pyx":675 * @@ -7381,7 +6853,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * elif header: */ __pyx_v_header_to_write = __pyx_v_template->samfile->header; - goto __pyx_L17; + goto __pyx_L20; } /* "csamtools.pyx":685 @@ -7401,8 +6873,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * * else: */ - __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->_buildHeader(__pyx_v_self, __pyx_v_header); - goto __pyx_L17; + __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->_buildHeader(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_header); + goto __pyx_L20; } /*else*/ { @@ -7451,7 +6923,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * header_to_write.n_targets = len(referencenames) */ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(((PyObject *)__pyx_t_5)); if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) { __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_14 = 0; __pyx_t_15 = NULL; @@ -7461,10 +6933,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) { + if (PyList_CheckExact(__pyx_t_8)) { if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_8)) break; __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) { + } else if (PyTuple_CheckExact(__pyx_t_8)) { if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_8)) break; __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++; } else { @@ -7537,10 +7009,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_15 = Py_TYPE(__pyx_t_5)->tp_iternext; } for (;;) { - if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_5)) { + if (PyList_CheckExact(__pyx_t_5)) { if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break; __pyx_t_8 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++; - } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_5)) { + } else if (PyTuple_CheckExact(__pyx_t_5)) { if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_5)) break; __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++; } else { @@ -7693,7 +7165,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) ) */ __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(((PyObject *)__pyx_t_5)); __Pyx_DECREF(__pyx_v_text); __pyx_v_text = ((PyObject *)__pyx_t_5); __pyx_t_5 = 0; @@ -7725,7 +7197,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_7 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(((PyObject *)__pyx_t_8)); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7); @@ -7765,7 +7237,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_INCREF(__pyx_v_text); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_text); __Pyx_GIVEREF(__pyx_v_text); @@ -7776,9 +7248,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_DECREF(__pyx_v_text); __pyx_v_text = __pyx_t_5; __pyx_t_5 = 0; - goto __pyx_L24; + goto __pyx_L27; } - __pyx_L24:; + __pyx_L27:; /* "csamtools.pyx":715 * text = ''.join(text) @@ -7842,9 +7314,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * header_to_write.hash = NULL */ memcpy(__pyx_v_header_to_write->text, __pyx_v_ctext, strlen(__pyx_v_ctext)); - goto __pyx_L27; + goto __pyx_L30; } - __pyx_L27:; + __pyx_L30:; /* "csamtools.pyx":723 * memcpy( header_to_write.text, ctext, strlen(ctext) ) @@ -7864,7 +7336,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools */ __pyx_v_header_to_write->rg2lib = NULL; } - __pyx_L17:; + __pyx_L20:; /* "csamtools.pyx":728 * # open file. Header gets written to file at the same time for bam files @@ -7890,7 +7362,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools */ __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->samfile = samopen(__pyx_t_20, __pyx_t_12, __pyx_v_header_to_write); + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, __pyx_v_header_to_write); /* "csamtools.pyx":730 * store = StderrStore() @@ -7931,10 +7403,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * elif mode[0] == "r": */ bam_header_destroy(__pyx_v_header_to_write); - goto __pyx_L28; + goto __pyx_L31; } - __pyx_L28:; - goto __pyx_L16; + __pyx_L31:; + goto __pyx_L19; } /* "csamtools.pyx":736 @@ -7968,7 +7440,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * not os.path.exists( filename ): * raise IOError( "file `%s` not found" % filename) */ - __pyx_t_1 = (!__pyx_v_self->isremote); + __pyx_t_1 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote); if (__pyx_t_1) { /* "csamtools.pyx":740 @@ -7987,7 +7459,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_INCREF(__pyx_v_filename); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename); __Pyx_GIVEREF(__pyx_v_filename); @@ -8018,7 +7490,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_32), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -8028,9 +7500,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L29; + goto __pyx_L32; } - __pyx_L29:; + __pyx_L32:; /* "csamtools.pyx":744 * @@ -8041,7 +7513,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools */ __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->samfile = samopen(__pyx_t_20, __pyx_t_12, NULL); + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, NULL); /* "csamtools.pyx":745 * # try to detect errors @@ -8050,7 +7522,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode) * */ - __pyx_t_1 = (__pyx_v_self->samfile == NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL); if (__pyx_t_1) { /* "csamtools.pyx":746 @@ -8063,7 +7535,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_33), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -8073,9 +7545,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L30; + goto __pyx_L33; } - __pyx_L30:; + __pyx_L33:; /* "csamtools.pyx":749 * @@ -8084,7 +7556,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * if self.samfile.header == NULL: * raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) */ - if (__pyx_v_self->isbam) { + if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) { /* "csamtools.pyx":750 * # bam files require a valid header @@ -8093,7 +7565,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) * else: */ - __pyx_t_1 = (__pyx_v_self->samfile->header == NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL); if (__pyx_t_1) { /* "csamtools.pyx":751 @@ -8106,7 +7578,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -8116,10 +7588,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L32; + goto __pyx_L35; } - __pyx_L32:; - goto __pyx_L31; + __pyx_L35:; + goto __pyx_L34; } /*else*/ { @@ -8132,7 +7604,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_t_10 = (__pyx_v_self->samfile->header == NULL); + __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL); __pyx_t_11 = __pyx_t_10; } else { __pyx_t_11 = __pyx_t_1; @@ -8149,7 +7621,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_35), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -8159,11 +7631,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L33; + goto __pyx_L36; } - __pyx_L33:; + __pyx_L36:; } - __pyx_L31:; + __pyx_L34:; /* "csamtools.pyx":759 * # disabled for autodetection to work @@ -8174,7 +7646,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools */ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_11) { - __pyx_t_1 = (__pyx_v_self->samfile->header->n_targets == 0); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0); __pyx_t_10 = __pyx_t_1; } else { __pyx_t_10 = __pyx_t_11; @@ -8191,7 +7663,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -8201,12 +7673,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L34; + goto __pyx_L37; } - __pyx_L34:; - goto __pyx_L16; + __pyx_L37:; + goto __pyx_L19; } - __pyx_L16:; + __pyx_L19:; /* "csamtools.pyx":762 * raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode) @@ -8215,7 +7687,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * raise IOError("could not open file `%s`" % filename ) * */ - __pyx_t_10 = (__pyx_v_self->samfile == NULL); + __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL); if (__pyx_t_10) { /* "csamtools.pyx":763 @@ -8228,7 +7700,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -8238,9 +7710,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L35; + goto __pyx_L38; } - __pyx_L35:; + __pyx_L38:; /* "csamtools.pyx":766 * @@ -8254,7 +7726,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (__pyx_t_10) { - __pyx_t_11 = __pyx_v_self->isbam; + __pyx_t_11 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam; } else { __pyx_t_11 = __pyx_t_10; } @@ -8267,7 +7739,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * if not os.path.exists(filename + b".bai"): * self.index = NULL */ - __pyx_t_11 = (!__pyx_v_self->isremote); + __pyx_t_11 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote); if (__pyx_t_11) { /* "csamtools.pyx":769 @@ -8288,7 +7760,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_7 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(((PyObject *)__pyx_t_5)); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = 0; @@ -8308,8 +7780,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * else: * # returns NULL if there is no index or index could not be opened */ - __pyx_v_self->index = NULL; - goto __pyx_L38; + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = NULL; + goto __pyx_L41; } /*else*/ { @@ -8321,7 +7793,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * raise IOError("error while opening index `%s` " % filename ) */ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->index = bam_index_load(__pyx_t_12); + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12); /* "csamtools.pyx":774 * # returns NULL if there is no index or index could not be opened @@ -8330,7 +7802,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * raise IOError("error while opening index `%s` " % filename ) * else: */ - __pyx_t_10 = (__pyx_v_self->index == NULL); + __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL); if (__pyx_t_10) { /* "csamtools.pyx":775 @@ -8343,7 +7815,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(((PyObject *)__pyx_t_5)); PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7)); __Pyx_GIVEREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; @@ -8353,12 +7825,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L39; + goto __pyx_L42; } - __pyx_L39:; + __pyx_L42:; } - __pyx_L38:; - goto __pyx_L37; + __pyx_L41:; + goto __pyx_L40; } /*else*/ { @@ -8370,7 +7842,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * raise IOError("error while opening index `%s` " % filename ) */ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->index = bam_index_load(__pyx_t_12); + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12); /* "csamtools.pyx":778 * else: @@ -8379,7 +7851,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * raise IOError("error while opening index `%s` " % filename ) * */ - __pyx_t_10 = (__pyx_v_self->index == NULL); + __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL); if (__pyx_t_10) { /* "csamtools.pyx":779 @@ -8392,7 +7864,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_5); + __Pyx_GOTREF(((PyObject *)__pyx_t_5)); PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7)); __Pyx_GIVEREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; @@ -8402,11 +7874,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L40; + goto __pyx_L43; } - __pyx_L40:; + __pyx_L43:; } - __pyx_L37:; + __pyx_L40:; /* "csamtools.pyx":781 * raise IOError("error while opening index `%s` " % filename ) @@ -8415,7 +7887,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * self.start_offset = bam_tell( self.samfile.x.bam ) * */ - __pyx_t_10 = (!__pyx_v_self->isstream); + __pyx_t_10 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream); if (__pyx_t_10) { /* "csamtools.pyx":782 @@ -8425,13 +7897,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools * * def gettid( self, reference ): */ - __pyx_v_self->start_offset = bam_tell(__pyx_v_self->samfile->x.bam); - goto __pyx_L41; + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset = bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam); + goto __pyx_L44; } - __pyx_L41:; - goto __pyx_L36; + __pyx_L44:; + goto __pyx_L39; } - __pyx_L36:; + __pyx_L39:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -8459,18 +7931,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_8gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n "; -static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("gettid (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_8gettid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_reference)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":784 * self.start_offset = bam_tell( self.samfile.x.bam ) * @@ -8479,7 +7939,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, Py * convert :term:`reference` name into numerical :term:`tid` */ -static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference) { +static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_4gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -8491,7 +7953,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("gettid", 0); + __Pyx_RefNannySetupContext("gettid"); __Pyx_TraceCall("gettid", __pyx_f[0], 784); __Pyx_INCREF(__pyx_v_reference); @@ -8502,7 +7964,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool * reference = _force_bytes(reference) * return pysam_reference2tid( self.samfile.header, reference ) */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -8516,9 +7978,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":791 * ''' @@ -8542,7 +8004,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool */ __Pyx_XDECREF(__pyx_r); __pyx_t_5 = PyBytes_AsString(__pyx_v_reference); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(__pyx_v_self->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -8563,18 +8025,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_10getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name."; -static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("getrname (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_10getrname(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_tid)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":794 * return pysam_reference2tid( self.samfile.header, reference ) * @@ -8583,7 +8033,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, * convert numerical :term:`tid` into :term:`reference` name.''' */ -static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid) { +static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_5getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name."; +static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -8595,7 +8047,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("getrname", 0); + __Pyx_RefNannySetupContext("getrname"); __Pyx_TraceCall("getrname", __pyx_f[0], 794); /* "csamtools.pyx":797 @@ -8605,7 +8057,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt * 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 ) ) */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -8619,9 +8071,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":798 * convert numerical :term:`tid` into :term:`reference` name.''' @@ -8634,7 +8086,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt __Pyx_GOTREF(__pyx_t_2); if (__Pyx_PyObject_IsTrue(__pyx_t_2)) { __Pyx_DECREF(__pyx_t_2); - __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_1, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -8652,10 +8104,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt * return _charptr_to_str(self.samfile.header.target_name[tid]) * */ - __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); 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+ PyObject *__pyx_t_10 = NULL; + PyObject *__pyx_t_11 = NULL; + Py_ssize_t __pyx_t_12; + int __pyx_t_13; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("_parseRegion"); + __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810); { PyObject* values[4] = {0,0,0,0}; @@ -8884,8 +8365,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_s values[3] = ((PyObject *)Py_None); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); @@ -8894,7 +8374,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_s default: goto __pyx_L5_argtuple_error; 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- PyObject *__pyx_t_10 = NULL; - PyObject *__pyx_t_11 = NULL; - Py_ssize_t __pyx_t_12; - int __pyx_t_13; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("_parseRegion", 0); - __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810); __Pyx_INCREF(__pyx_v_reference); __Pyx_INCREF(__pyx_v_region); @@ -9045,14 +8486,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c * except OverflowError: * raise ValueError( 'start out of range (%i)' % start ) */ - __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L7_error;} __pyx_v_rstart = __pyx_t_6; 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if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} + __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_10)); - __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} - __Pyx_GOTREF(__pyx_t_11); + __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_11)); PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10)); __Pyx_GIVEREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} + __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;} __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0; __Pyx_Raise(__pyx_t_10, 0, 0, 0); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - goto __pyx_L5_exception_handled; + goto __pyx_L8_exception_handled; } - __pyx_L6_except_error:; + __pyx_L9_except_error:; __Pyx_XGIVEREF(__pyx_t_3); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_XGIVEREF(__pyx_t_5); __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5); goto __pyx_L1_error; - __pyx_L5_exception_handled:; + __pyx_L8_exception_handled:; __Pyx_XGIVEREF(__pyx_t_3); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_XGIVEREF(__pyx_t_5); __Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5); - __pyx_L11_try_end:; + __pyx_L14_try_end:; } - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":842 * raise ValueError( 'start out of range (%i)' % start ) @@ -9146,14 +8587,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c * except OverflowError: * raise ValueError( 'end out of range (%i)' % end ) */ - __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L15_error;} + __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L18_error;} __pyx_v_rend = __pyx_t_6; } __Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0; __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; - goto __pyx_L22_try_end; - __pyx_L15_error:; + goto __pyx_L25_try_end; + __pyx_L18_error:; __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0; __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -9170,7 +8611,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError); if (__pyx_t_7) { __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;} + if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_GOTREF(__pyx_t_8); __Pyx_GOTREF(__pyx_t_1); @@ -9182,40 +8623,40 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c * * if region: */ - __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;} + __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_10)); - __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;} - __Pyx_GOTREF(__pyx_t_11); + __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_11)); PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10)); __Pyx_GIVEREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; - __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;} + __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;} __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0; __Pyx_Raise(__pyx_t_10, 0, 0, 0); __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - goto __pyx_L16_exception_handled; + goto __pyx_L19_exception_handled; } - __pyx_L17_except_error:; + __pyx_L20_except_error:; __Pyx_XGIVEREF(__pyx_t_5); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_XGIVEREF(__pyx_t_3); __Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3); goto __pyx_L1_error; - __pyx_L16_exception_handled:; + __pyx_L19_exception_handled:; __Pyx_XGIVEREF(__pyx_t_5); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_XGIVEREF(__pyx_t_3); __Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3); - __pyx_L22_try_end:; + __pyx_L25_try_end:; } - goto __pyx_L14; + goto __pyx_L17; } - __pyx_L14:; + __pyx_L17:; /* "csamtools.pyx":848 * raise ValueError( 'end out of range (%i)' % end ) @@ -9253,7 +8694,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_43)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_43)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43)); @@ -9293,7 +8734,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9); __Pyx_GIVEREF(__pyx_t_9); __pyx_t_9 = 0; @@ -9306,9 +8747,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_v_rstart = __pyx_t_6; - goto __pyx_L26; + goto __pyx_L29; } - __pyx_L26:; + __pyx_L29:; /* "csamtools.pyx":853 * reference = parts[0] @@ -9323,7 +8764,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_parts, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; @@ -9333,12 +8774,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_v_rend = __pyx_t_6; - goto __pyx_L27; + goto __pyx_L30; } - __pyx_L27:; - goto __pyx_L25; + __pyx_L30:; + goto __pyx_L28; } - __pyx_L25:; + __pyx_L28:; /* "csamtools.pyx":855 * if len(parts) >= 3: rend = int(parts[2]) @@ -9354,9 +8795,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_INCREF(((PyObject *)__pyx_k_tuple_44)); __pyx_r = ((PyObject *)__pyx_k_tuple_44); goto __pyx_L0; - goto __pyx_L28; + goto __pyx_L31; } - __pyx_L28:; + __pyx_L31:; /* "csamtools.pyx":857 * if not reference: return 0, 0, 0, 0 @@ -9365,10 +8806,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); __Pyx_INCREF(__pyx_v_reference); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_reference); __Pyx_GIVEREF(__pyx_v_reference); @@ -9392,7 +8833,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), __pyx_v_reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -9402,9 +8843,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L29; + goto __pyx_L32; } - __pyx_L29:; + __pyx_L32:; /* "csamtools.pyx":859 * rtid = self.gettid( reference ) @@ -9420,7 +8861,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_9 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_9); @@ -9431,7 +8872,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_GOTREF(((PyObject *)__pyx_t_9)); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9)); __Pyx_GIVEREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; @@ -9441,9 +8882,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_Raise(__pyx_t_9, 0, 0, 0); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L30; + goto __pyx_L33; } - __pyx_L30:; + __pyx_L33:; /* "csamtools.pyx":860 * if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) @@ -9464,7 +8905,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -9474,9 +8915,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L31; + goto __pyx_L34; } - __pyx_L31:; + __pyx_L34:; /* "csamtools.pyx":861 * if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) @@ -9497,7 +8938,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_GOTREF(((PyObject *)__pyx_t_9)); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9)); __Pyx_GIVEREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; @@ -9507,9 +8948,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __Pyx_Raise(__pyx_t_9, 0, 0, 0); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L32; + goto __pyx_L35; } - __pyx_L32:; + __pyx_L35:; /* "csamtools.pyx":863 * if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend ) @@ -9526,7 +8967,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c __pyx_t_8 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_GOTREF(((PyObject *)__pyx_t_10)); __Pyx_INCREF(__pyx_int_1); PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_int_1); __Pyx_GIVEREF(__pyx_int_1); @@ -9563,18 +9004,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_14reset[] = "Samfile.reset(self)\nreset file position to beginning of read section."; -static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("reset (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_14reset(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":865 * return 1, rtid, rstart, rend * @@ -9583,7 +9012,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CY * return self.seek( self.start_offset, 0 ) */ -static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_7reset[] = "Samfile.reset(self)\nreset file position to beginning of read section."; +static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -9593,7 +9024,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtool const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("reset", 0); + __Pyx_RefNannySetupContext("reset"); __Pyx_TraceCall("reset", __pyx_f[0], 865); /* "csamtools.pyx":867 @@ -9604,12 +9035,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtool * def seek( self, uint64_t offset, int where = 0): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(__pyx_v_self->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __Pyx_INCREF(__pyx_int_0); @@ -9639,29 +9070,44 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtool return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_16seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n "; -static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +/* "csamtools.pyx":869 + * return self.seek( self.start_offset, 0 ) + * + * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<< + * ''' + * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`. + */ + +static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_8seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { uint64_t __pyx_v_offset; int __pyx_v_where; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0}; - PyObject *__pyx_r = 0; + PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("seek (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("seek"); + __Pyx_TraceCall("seek", __pyx_f[0], 869); { PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset); if (likely(values[0])) kw_args--; @@ -9673,11 +9119,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyO } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - } - if (values[1]) { - } else { - __pyx_v_where = ((int)0); + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -9702,32 +9144,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyO __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_9csamtools_7Samfile_16seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_offset, __pyx_v_where); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "csamtools.pyx":869 - * return self.seek( self.start_offset, 0 ) - * - * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<< - * ''' - * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`. - */ - -static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where) { - PyObject *__pyx_r = NULL; - __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; - PyObject *__pyx_t_2 = NULL; - int __pyx_t_3; - int __pyx_t_4; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("seek", 0); - __Pyx_TraceCall("seek", __pyx_f[0], 869); /* "csamtools.pyx":874 * ''' @@ -9736,7 +9152,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools * raise ValueError( "I/O operation on closed file" ) * if not self.isbam: */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -9758,9 +9174,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":876 * if not self._isOpen(): @@ -9769,7 +9185,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools * raise NotImplementedError("seek only available in bam files") * if self.isstream: */ - __pyx_t_4 = (!__pyx_v_self->isbam); + __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam); if (__pyx_t_4) { /* "csamtools.pyx":877 @@ -9784,9 +9200,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L7; } - __pyx_L4:; + __pyx_L7:; /* "csamtools.pyx":878 * if not self.isbam: @@ -9795,7 +9211,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools * raise OSError("seek no available in streams") * */ - if (__pyx_v_self->isstream) { + if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) { /* "csamtools.pyx":879 * raise NotImplementedError("seek only available in bam files") @@ -9809,9 +9225,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + goto __pyx_L8; } - __pyx_L5:; + __pyx_L8:; /* "csamtools.pyx":881 * raise OSError("seek no available in streams") @@ -9821,7 +9237,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools * def tell( self ): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(__pyx_v_self->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -9841,18 +9257,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_18tell[] = "Samfile.tell(self)\n\n return current file position\n "; -static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("tell (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_18tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":883 * return bam_seek( self.samfile.x.bam, offset, where ) * @@ -9861,7 +9265,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYT * return current file position */ -static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_9tell[] = "Samfile.tell(self)\n\n return current file position\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -9872,7 +9278,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("tell", 0); + __Pyx_RefNannySetupContext("tell"); __Pyx_TraceCall("tell", __pyx_f[0], 883); /* "csamtools.pyx":887 @@ -9882,7 +9288,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools * raise ValueError( "I/O operation on closed file" ) * if not self.isbam: */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -9904,9 +9310,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":889 * if not self._isOpen(): @@ -9915,7 +9321,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools * raise NotImplementedError("seek only available in bam files") * */ - __pyx_t_4 = (!__pyx_v_self->isbam); + __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam); if (__pyx_t_4) { /* "csamtools.pyx":890 @@ -9930,9 +9336,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":892 * raise NotImplementedError("seek only available in bam files") @@ -9942,7 +9348,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools * def fetch( self, */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(__pyx_v_self->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -9962,20 +9368,52 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_20fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n ordered by reference sequence, which will not necessarily be the order within the file.\n\n If *until_eof* is given, all reads from the current file position will be returned\n in order as they are within the file. Using this option will also fetch unmapped reads.\n\n If only *reference* is set, all reads aligned to *reference* will be fetched.\n\n The method returns an iterator of type :class:`pysam.IteratorRow` unless\n a *callback is provided. If *callback* is given, the callback will be executed\n for each position within the :term:`region`. Note that callbacks currently work\n only, if *region* or *reference* is given.\n\n Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n "; -static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +/* "csamtools.pyx":894 + * return bam_tell( self.samfile.x.bam ) + * + * def fetch( self, # <<<<<<<<<<<<<< + * reference = None, + * start = None, + */ + +static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_10fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n ordered by reference sequence, which will not necessarily be the order within the file.\n\n If *until_eof* is given, all reads from the current file position will be returned\n in order as they are within the file. Using this option will also fetch unmapped reads.\n\n If only *reference* is set, all reads aligned to *reference* will be fetched.\n\n The method returns an iterator of type :class:`pysam.IteratorRow` unless\n a *callback is provided. If *callback* is given, the callback will be executed\n for each position within the :term:`region`. Note that callbacks currently work\n only, if *region* or *reference* is given.\n\n Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_region = 0; PyObject *__pyx_v_callback = 0; PyObject *__pyx_v_until_eof = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0}; - PyObject *__pyx_r = 0; + int __pyx_v_rtid; + int __pyx_v_rstart; + int __pyx_v_rend; + int __pyx_v_has_coord; + int __pyx_v_reopen; + PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("fetch (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *(*__pyx_t_9)(PyObject *); + int __pyx_t_10; + int __pyx_t_11; + int __pyx_t_12; + int __pyx_t_13; + int __pyx_t_14; + int __pyx_t_15; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("fetch"); + __Pyx_TraceCall("fetch", __pyx_f[0], 894); { PyObject* values[6] = {0,0,0,0,0,0}; @@ -10026,8 +9464,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py values[5] = __pyx_k_54; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5); case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); @@ -10038,7 +9475,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference); @@ -10071,7 +9508,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -10100,48 +9537,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_9csamtools_7Samfile_20fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_until_eof); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "csamtools.pyx":894 - * return bam_tell( self.samfile.x.bam ) - * - * def fetch( self, # <<<<<<<<<<<<<< - * reference = None, - * start = None, - */ - -static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof) { - int __pyx_v_rtid; - int __pyx_v_rstart; - int __pyx_v_rend; - int __pyx_v_has_coord; - int __pyx_v_reopen; - PyObject *__pyx_r = NULL; - __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; - PyObject *__pyx_t_2 = NULL; - int __pyx_t_3; - int __pyx_t_4; - PyObject *__pyx_t_5 = NULL; - PyObject *__pyx_t_6 = NULL; - PyObject *__pyx_t_7 = NULL; - PyObject *__pyx_t_8 = NULL; - PyObject *(*__pyx_t_9)(PyObject *); - int __pyx_t_10; - int __pyx_t_11; - int __pyx_t_12; - int __pyx_t_13; - int __pyx_t_14; - int __pyx_t_15; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("fetch", 0); - __Pyx_TraceCall("fetch", __pyx_f[0], 894); /* "csamtools.pyx":924 * cdef int rtid, rstart, rend, has_coord @@ -10150,7 +9545,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * raise ValueError( "I/O operation on closed file" ) * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -10172,9 +9567,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":927 * raise ValueError( "I/O operation on closed file" ) @@ -10183,10 +9578,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * * if self.isstream: reopen = False */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_reference); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference); __Pyx_GIVEREF(__pyx_v_reference); @@ -10237,23 +9632,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext; - index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed; + index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_1); - index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed; + index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed; + index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_6); - index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed; + index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_7); if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - goto __pyx_L5_unpacking_done; - __pyx_L4_unpacking_failed:; + goto __pyx_L8_unpacking_done; + __pyx_L7_unpacking_failed:; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L5_unpacking_done:; + __pyx_L8_unpacking_done:; } __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -10275,9 +9670,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * else: reopen = True * */ - if (__pyx_v_self->isstream) { + if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) { __pyx_v_reopen = 0; - goto __pyx_L6; + goto __pyx_L9; } /*else*/ { @@ -10290,7 +9685,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool */ __pyx_v_reopen = 1; } - __pyx_L6:; + __pyx_L9:; /* "csamtools.pyx":932 * else: reopen = True @@ -10299,7 +9694,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * if not until_eof and not self._hasIndex() and not self.isremote: * raise ValueError( "fetch called on bamfile without index" ) */ - if (__pyx_v_self->isbam) { + if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) { /* "csamtools.pyx":933 * @@ -10311,7 +9706,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = (!__pyx_t_4); if (__pyx_t_3) { - __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); @@ -10320,7 +9715,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_14 = (!__pyx_t_4); if (__pyx_t_14) { - __pyx_t_4 = (!__pyx_v_self->isremote); + __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote); __pyx_t_15 = __pyx_t_4; } else { __pyx_t_15 = __pyx_t_14; @@ -10343,9 +9738,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L8; + goto __pyx_L11; } - __pyx_L8:; + __pyx_L11:; /* "csamtools.pyx":936 * raise ValueError( "fetch called on bamfile without index" ) @@ -10371,9 +9766,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L10; + goto __pyx_L13; } - __pyx_L10:; + __pyx_L13:; /* "csamtools.pyx":938 * if callback: @@ -10382,7 +9777,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * return bam_fetch(self.samfile.x.bam, * self.index, */ - __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); @@ -10396,9 +9791,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L11; + goto __pyx_L14; } - __pyx_L11:; + __pyx_L14:; /* "csamtools.pyx":939 * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) @@ -10416,12 +9811,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * else: * if has_coord: */ - __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyInt_FromLong(bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - goto __pyx_L9; + goto __pyx_L12; } /*else*/ { @@ -10449,10 +9844,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self)); - __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_INCREF(__pyx_v_self); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self); + __Pyx_GIVEREF(__pyx_v_self); PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_7); @@ -10468,14 +9863,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_GOTREF(__pyx_t_7); if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; __pyx_r = __pyx_t_7; __pyx_t_7 = 0; goto __pyx_L0; - goto __pyx_L12; + goto __pyx_L15; } /*else*/ { @@ -10498,24 +9893,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool */ __Pyx_XDECREF(__pyx_r); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self)); - __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); + __Pyx_INCREF(__pyx_v_self); + PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self); + __Pyx_GIVEREF(__pyx_v_self); __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0; - goto __pyx_L13; + goto __pyx_L16; } /*else*/ { @@ -10528,10 +9923,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool */ __Pyx_XDECREF(__pyx_r); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self)); - __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); + __Pyx_INCREF(__pyx_v_self); + PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self); + __Pyx_GIVEREF(__pyx_v_self); __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAllRefs)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; @@ -10539,12 +9934,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __pyx_t_6 = 0; goto __pyx_L0; } - __pyx_L13:; + __pyx_L16:; } - __pyx_L12:; + __pyx_L15:; } - __pyx_L9:; - goto __pyx_L7; + __pyx_L12:; + goto __pyx_L10; } /*else*/ { @@ -10569,9 +9964,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_6, 0, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L14; + goto __pyx_L17; } - __pyx_L14:; + __pyx_L17:; /* "csamtools.pyx":959 * raise ValueError ("fetching by region is not available for sam files" ) @@ -10595,9 +9990,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_6, 0, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L15; + goto __pyx_L18; } - __pyx_L15:; + __pyx_L18:; /* "csamtools.pyx":962 * raise NotImplementedError( "callback not implemented yet" ) @@ -10606,7 +10001,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * raise ValueError( "fetch called for samfile without header") * */ - __pyx_t_3 = (__pyx_v_self->samfile->header == NULL); + __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL); if (__pyx_t_3) { /* "csamtools.pyx":963 @@ -10621,9 +10016,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_6, 0, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L16; + goto __pyx_L19; } - __pyx_L16:; + __pyx_L19:; /* "csamtools.pyx":967 * # check if targets are defined @@ -10632,7 +10027,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool * warnings.warn( "fetch called for samfile without header") * */ - __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0); + __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0); if (__pyx_t_3) { /* "csamtools.pyx":968 @@ -10651,9 +10046,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - goto __pyx_L17; + goto __pyx_L20; } - __pyx_L17:; + __pyx_L20:; /* "csamtools.pyx":970 * warnings.warn( "fetch called for samfile without header") @@ -10664,17 +10059,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool */ __Pyx_XDECREF(__pyx_r); __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self)); - __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __Pyx_INCREF(__pyx_v_self); + PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self); + __Pyx_GIVEREF(__pyx_v_self); __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; - __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; @@ -10682,7 +10077,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool __pyx_t_7 = 0; goto __pyx_L0; } - __pyx_L7:; + __pyx_L10:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -10702,23 +10097,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_22mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n "; -static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("mate (wrapper)", 0); - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_9csamtools_7Samfile_22mate(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)); - goto __pyx_L0; - __pyx_L1_error:; - __pyx_r = NULL; - __pyx_L0:; - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":972 * return IteratorRowAll( self, reopen=reopen ) * @@ -10727,7 +10105,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyO * '''return the mate of :class:`AlignedRead` *read*. */ -static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read) { +static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_11mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) { uint32_t __pyx_v_flag; __pyx_t_9csamtools_MateData __pyx_v_mate_data; int __pyx_v_x; @@ -10741,8 +10121,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("mate", 0); + __Pyx_RefNannySetupContext("mate"); __Pyx_TraceCall("mate", __pyx_f[0], 972); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":985 * @@ -10751,7 +10132,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools * * if flag & BAM_FPAIRED == 0: */ - __pyx_v_flag = __pyx_v_read->_delegate->core.flag; + __pyx_v_flag = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.flag; /* "csamtools.pyx":987 * cdef uint32_t flag = read._delegate.core.flag @@ -10770,13 +10151,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools * if flag & BAM_FMUNMAP != 0: * raise ValueError( "mate %s: is unmapped" % (read.qname)) */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_69), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_3)); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3)); __Pyx_GIVEREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; @@ -10786,9 +10167,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":989 * if flag & BAM_FPAIRED == 0: @@ -10807,13 +10188,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools * * cdef MateData mate_data */ - __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_70), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2)); __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; @@ -10823,9 +10204,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":994 * cdef MateData mate_data @@ -10834,7 +10215,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools * mate_data.mate = NULL * # xor flags to get the other mate */ - __pyx_v_mate_data.name = ((char *)bam1_qname(__pyx_v_read->_delegate)); + __pyx_v_mate_data.name = ((char *)bam1_qname(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate)); /* "csamtools.pyx":995 * @@ -10870,7 +10251,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools * * if mate_data.mate == NULL: */ - bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback); + bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mtid, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos, (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback); /* "csamtools.pyx":1008 * mate_callback ) @@ -10894,9 +10275,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools __Pyx_Raise(__pyx_t_2, 0, 0, 0); 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The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not allow random access. If *region* or *reference* are given,\n an exception is raised.\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_region = 0; PyObject *__pyx_v_until_eof = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0}; - PyObject *__pyx_r = 0; + int __pyx_v_rtid; + int __pyx_v_rstart; + int __pyx_v_rend; + int __pyx_v_counter; + PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("count (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *(*__pyx_t_9)(PyObject *); + int __pyx_t_10; + int __pyx_t_11; + int __pyx_t_12; + int __pyx_t_13; + int __pyx_t_14; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("count"); + __Pyx_TraceCall("count", __pyx_f[0], 1015); { PyObject* values[5] = {0,0,0,0,0}; @@ -11001,8 +10412,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py values[4] = __pyx_k_73; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); @@ -11012,7 +10422,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference); @@ -11040,7 +10450,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -11067,46 +10477,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_9csamtools_7Samfile_24count(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_until_eof); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "csamtools.pyx":1015 - * return dest - * - * def count( self, # <<<<<<<<<<<<<< - * reference = None, - * start = None, - */ - -static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof) { - int __pyx_v_rtid; - int __pyx_v_rstart; - int __pyx_v_rend; - int __pyx_v_counter; - PyObject *__pyx_r = NULL; - __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; - PyObject *__pyx_t_2 = NULL; - int __pyx_t_3; - int __pyx_t_4; - PyObject *__pyx_t_5 = NULL; - PyObject *__pyx_t_6 = NULL; - PyObject *__pyx_t_7 = NULL; - PyObject *__pyx_t_8 = NULL; - PyObject *(*__pyx_t_9)(PyObject *); - int __pyx_t_10; - int __pyx_t_11; - int __pyx_t_12; - int __pyx_t_13; - int __pyx_t_14; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("count", 0); - __Pyx_TraceCall("count", __pyx_f[0], 1015); __Pyx_INCREF(__pyx_v_region); /* "csamtools.pyx":1033 @@ -11116,7 +10486,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool * raise ValueError( "I/O operation on closed file" ) * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -11138,9 +10508,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":1036 * raise ValueError( "I/O operation on closed file" ) @@ -11149,10 +10519,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool * * cdef int counter */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_reference); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference); __Pyx_GIVEREF(__pyx_v_reference); @@ -11203,23 +10573,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext; - index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed; + index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_1); - index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed; + index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed; + index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_6); - index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed; + index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_7); if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - goto __pyx_L5_unpacking_done; - __pyx_L4_unpacking_failed:; + goto __pyx_L8_unpacking_done; + __pyx_L7_unpacking_failed:; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L5_unpacking_done:; + __pyx_L8_unpacking_done:; } __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -11250,7 +10620,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool * if not until_eof and not self._hasIndex() and not self.isremote: * raise ValueError( "fetch called on bamfile without index" ) */ - if (__pyx_v_self->isbam) { + if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) { /* "csamtools.pyx":1042 * @@ -11262,7 +10632,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = (!__pyx_t_4); if (__pyx_t_3) { - __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); @@ -11271,7 +10641,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_13 = (!__pyx_t_4); if (__pyx_t_13) { - __pyx_t_4 = (!__pyx_v_self->isremote); + __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote); __pyx_t_14 = __pyx_t_4; } else { __pyx_t_14 = __pyx_t_13; @@ -11294,9 +10664,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L7; + goto __pyx_L10; } - __pyx_L7:; + __pyx_L10:; /* "csamtools.pyx":1045 * raise ValueError( "fetch called on bamfile without index" ) @@ -11321,9 +10691,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L8; + goto __pyx_L11; } - __pyx_L8:; + __pyx_L11:; /* "csamtools.pyx":1047 * if not region: @@ -11332,7 +10702,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool * bam_fetch(self.samfile.x.bam, * self.index, */ - __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); @@ -11346,9 +10716,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L9; + goto __pyx_L12; } - __pyx_L9:; + __pyx_L12:; /* "csamtools.pyx":1054 * rend, @@ -11357,7 +10727,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool * return counter * else: */ - bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback); + bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback); /* "csamtools.pyx":1055 * &counter, @@ -11372,7 +10742,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - goto __pyx_L6; + goto __pyx_L9; } /*else*/ { @@ -11389,7 +10759,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_L6:; + __pyx_L9:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -11410,20 +10780,50 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_26pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed\n for each column within the :term:`region`.\n\n Note that :term:`SAM` formatted files do not allow random access.\n In these files, if a *region* or *reference* are given an exception is raised.\n\n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances.\n Possible options for the stepper are\n\n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask if mask=True.\n\n max_depth\n Maximum read depth permitted. The default limit is *8000*.\n\n truncate\n By default, the samtools pileup engine outputs all reads overlapping a region (see note below).\n If truncate is True and a region is given, only output columns in the exact region\n specificied.\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the\n first base of the first read *not* necessarily the first base of the region used in the query.\n\n "; -static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +/* "csamtools.pyx":1059 + * raise ValueError ("count for a region is not available for sam files" ) + * + * def pileup( self, # <<<<<<<<<<<<<< + * reference = None, + * start = None, + */ + +static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_13pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n ordered by :term:`reference` sequence, which will not necessarily be the order within the file.\n\n The method returns an iterator of type :class:`pysam.IteratorColumn` unless\n a *callback is provided. If a *callback* is given, the callback will be executed\n for each column within the :term:`region`.\n\n Note that :term:`SAM` formatted files do not allow random access.\n In these files, if a *region* or *reference* are given an exception is raised.\n\n Optional *kwargs* to the iterator:\n\n stepper\n The stepper controlls how the iterator advances.\n Possible options for the stepper are\n\n ``all``\n use all reads for pileup.\n ``samtools``\n same filter and read processing as in :term:`csamtools` pileup\n\n fastafile\n A :class:`FastaFile` object\n\n mask\n Skip all reads with bits set in mask if mask=True.\n\n max_depth\n Maximum read depth permitted. The default limit is *8000*.\n\n truncate\n By default, the samtools pileup engine outputs all reads overlapping a region (see note below).\n If truncate is True and a region is given, only output columns in the exact region\n specificied.\n\n .. note::\n\n *all* reads which overlap the region are returned. The first base returned will be the\n first base of the first read *not* necessarily the first base of the region used in the query.\n\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_reference = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; PyObject *__pyx_v_region = 0; PyObject *__pyx_v_callback = 0; PyObject *__pyx_v_kwargs = 0; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0}; - PyObject *__pyx_r = 0; + int __pyx_v_rtid; + int __pyx_v_rstart; + int __pyx_v_rend; + int __pyx_v_has_coord; + bam_plbuf_t *__pyx_v_buf; + PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("pileup (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + PyObject *__pyx_t_8 = NULL; + PyObject *(*__pyx_t_9)(PyObject *); + int __pyx_t_10; + int __pyx_t_11; + int __pyx_t_12; + int __pyx_t_13; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("pileup"); + __Pyx_TraceCall("pileup", __pyx_f[0], 1059); __pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL; __Pyx_GOTREF(__pyx_v_kwargs); { @@ -11475,8 +10875,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P values[4] = ((PyObject *)Py_None); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); @@ -11486,7 +10885,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference); @@ -11514,7 +10913,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -11542,47 +10941,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_9csamtools_7Samfile_26pileup(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_kwargs); - __Pyx_XDECREF(__pyx_v_kwargs); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "csamtools.pyx":1059 - * raise ValueError ("count for a region is not available for sam files" ) - * - * def pileup( self, # <<<<<<<<<<<<<< - * reference = None, - * start = None, - */ - -static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs) { - int __pyx_v_rtid; - int __pyx_v_rstart; - int __pyx_v_rend; - int __pyx_v_has_coord; - bam_plbuf_t *__pyx_v_buf; - PyObject *__pyx_r = NULL; - __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; - PyObject *__pyx_t_2 = NULL; - int __pyx_t_3; - int __pyx_t_4; - PyObject *__pyx_t_5 = NULL; - PyObject *__pyx_t_6 = NULL; - PyObject *__pyx_t_7 = NULL; - PyObject *__pyx_t_8 = NULL; - PyObject *(*__pyx_t_9)(PyObject *); - int __pyx_t_10; - int __pyx_t_11; - int __pyx_t_12; - int __pyx_t_13; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("pileup", 0); - __Pyx_TraceCall("pileup", __pyx_f[0], 1059); /* "csamtools.pyx":1115 * cdef bam_plbuf_t *buf @@ -11591,7 +10949,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo * raise ValueError( "I/O operation on closed file" ) * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -11613,9 +10971,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":1118 * raise ValueError( "I/O operation on closed file" ) @@ -11624,10 +10982,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo * * if self.isbam: */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_reference); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference); __Pyx_GIVEREF(__pyx_v_reference); @@ -11678,23 +11036,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext; - index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed; + index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_1); - index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed; + index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed; + index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_6); - index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed; + index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_7); if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - goto __pyx_L5_unpacking_done; - __pyx_L4_unpacking_failed:; + goto __pyx_L8_unpacking_done; + __pyx_L7_unpacking_failed:; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L5_unpacking_done:; + __pyx_L8_unpacking_done:; } __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -11716,7 +11074,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo * if not self._hasIndex(): raise ValueError( "no index available for pileup" ) * */ - if (__pyx_v_self->isbam) { + if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) { /* "csamtools.pyx":1121 * @@ -11725,7 +11083,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo * * if callback: */ - __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); @@ -11739,9 +11097,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L7; + goto __pyx_L10; } - __pyx_L7:; + __pyx_L10:; /* "csamtools.pyx":1123 * if not self._hasIndex(): raise ValueError( "no index available for pileup" ) @@ -11767,9 +11125,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L9; + goto __pyx_L12; } - __pyx_L9:; + __pyx_L12:; /* "csamtools.pyx":1126 * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) @@ -11787,7 +11145,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo * * # finalize pileup */ - bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback); + bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback); /* "csamtools.pyx":1132 * @@ -11806,7 +11164,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo * if has_coord: */ bam_plbuf_destroy(__pyx_v_buf); - goto __pyx_L8; + goto __pyx_L11; } /*else*/ { @@ -11828,19 +11186,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo */ __Pyx_XDECREF(__pyx_r); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self)); - __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); - - /* "csamtools.pyx":1140 - * start = rstart, - * end = rend, - * **kwargs ) # <<<<<<<<<<<<<< - * else: - * return IteratorColumnAllRefs(self, **kwargs ) - */ - __pyx_t_5 = PyDict_Copy(((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); + __Pyx_INCREF(__pyx_v_self); + PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self); + __Pyx_GIVEREF(__pyx_v_self); 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if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __Pyx_INCREF(__pyx_v_self); + PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self); + __Pyx_GIVEREF(__pyx_v_self); + __pyx_t_5 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; - __pyx_r = __pyx_t_7; - __pyx_t_7 = 0; + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; goto __pyx_L0; } - __pyx_L10:; + __pyx_L13:; } - __pyx_L8:; - goto __pyx_L6; + __pyx_L11:; + goto __pyx_L9; } /*else*/ { @@ -11935,13 +11282,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo * * def close( self ): */ - __pyx_t_7 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); 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__Pyx_XGIVEREF(__pyx_r); __Pyx_TraceReturn(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_28close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`."; -static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("close (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_28close(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1147 * raise NotImplementedError( "pileup of samfiles not implemented yet" ) * @@ -11981,12 +11317,14 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CY * closes the :class:`pysam.Samfile`.''' */ -static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_14close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`."; +static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("close", 0); + __Pyx_RefNannySetupContext("close"); __Pyx_TraceCall("close", __pyx_f[0], 1147); /* "csamtools.pyx":1150 @@ -11996,7 +11334,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool * samclose( self.samfile ) * bam_index_destroy(self.index); */ - __pyx_t_1 = (__pyx_v_self->samfile != NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL); if (__pyx_t_1) { /* "csamtools.pyx":1151 @@ -12006,7 +11344,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool * bam_index_destroy(self.index); * self.samfile = NULL */ - samclose(__pyx_v_self->samfile); + samclose(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile); /* "csamtools.pyx":1152 * if self.samfile != NULL: @@ -12015,7 +11353,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool * self.samfile = NULL * */ - bam_index_destroy(__pyx_v_self->index); + bam_index_destroy(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index); /* "csamtools.pyx":1153 * samclose( self.samfile ) @@ -12024,10 +11362,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool * * def __dealloc__( self ): */ - __pyx_v_self->samfile = NULL; - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); __Pyx_XGIVEREF(__pyx_r); @@ -12036,15 +11374,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool return __pyx_r; } -/* Python wrapper */ -static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self) { - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_9csamtools_7Samfile_30__dealloc__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); -} - /* "csamtools.pyx":1155 * self.samfile = NULL * @@ -12053,7 +11382,8 @@ static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self) { * # note: no doc string */ -static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; @@ -12062,7 +11392,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__dealloc__", 0); + __Pyx_RefNannySetupContext("__dealloc__"); __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1155); /* "csamtools.pyx":1159 @@ -12072,7 +11402,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo * bam_destroy1(self.b) * if self._filename != NULL: free( self._filename ) */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -12086,7 +11416,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo * if self._filename != NULL: free( self._filename ) * */ - bam_destroy1(__pyx_v_self->b); + bam_destroy1(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b); /* "csamtools.pyx":1161 * self.close() @@ -12095,12 +11425,12 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo * * cpdef int write( self, AlignedRead read ) except -1: */ - __pyx_t_3 = (__pyx_v_self->_filename != NULL); + __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL); if (__pyx_t_3) { - free(__pyx_v_self->_filename); - goto __pyx_L3; + free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename); + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; goto __pyx_L0; __pyx_L1_error:; @@ -12120,7 +11450,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo * write a single :class:`pysam.AlignedRead` to disk. */ -static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) { int __pyx_r; __Pyx_RefNannyDeclarations @@ -12134,7 +11464,7 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("write", 0); + __Pyx_RefNannySetupContext("write"); __Pyx_TraceCall("write", __pyx_f[0], 1163); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; @@ -12142,9 +11472,9 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_9csamtools_7Samfile_33write)) { + if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (void *)&__pyx_pf_9csamtools_7Samfile_16write)) { __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_INCREF(((PyObject *)__pyx_v_read)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_read)); __Pyx_GIVEREF(((PyObject *)__pyx_v_read)); @@ -12214,23 +11544,6 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_32write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n "; 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/*proto*/ +static char __pyx_doc_9csamtools_7Samfile_16write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n "; +static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -12247,10 +11562,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtool const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("write", 0); + __Pyx_RefNannySetupContext("write"); __Pyx_TraceCall("write", __pyx_f[0], 1163); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->write(__pyx_v_self, __pyx_v_read, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->write(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read), 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -12269,18 +11585,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtool return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_34__enter__[] = "Samfile.__enter__(self)"; -static PyObject *__pyx_pw_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { - PyObject *__pyx_r = 0; 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -12447,17 +11742,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamt return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); 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} -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_11nreferences___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1194 * property nreferences: * '''number of :term:`reference` sequences in the file.''' @@ -12552,7 +11826,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *_ * return self.samfile.header.n_targets */ -static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -12587,9 +11862,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1196 * def __get__(self): @@ -12599,7 +11874,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx * property references: */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -12619,17 +11894,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_10references___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1200 * property references: * """tuple with the names of :term:`reference` sequences.""" @@ -12638,7 +11902,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__ * t = [] */ -static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self) { PyObject *__pyx_v_t = NULL; long __pyx_v_x; PyObject *__pyx_r = NULL; @@ -12653,7 +11918,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 1200); /* "csamtools.pyx":1201 @@ -12663,7 +11928,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ * t = [] * for x from 0 <= x < self.samfile.header.n_targets: */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -12677,9 +11942,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1202 * def __get__(self): @@ -12689,7 +11954,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ * t.append( _charptr_to_str(self.samfile.header.target_name[x]) ) */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_t = __pyx_t_2; __pyx_t_2 = 0; @@ -12700,7 +11965,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ * t.append( _charptr_to_str(self.samfile.header.target_name[x]) ) * return tuple(t) */ - __pyx_t_5 = __pyx_v_self->samfile->header->n_targets; + __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets; for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) { /* "csamtools.pyx":1204 @@ -12710,7 +11975,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ * return tuple(t) * */ - __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -12724,6 +11992,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ * property lengths: */ __Pyx_XDECREF(__pyx_r); + if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); @@ -12745,17 +12016,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_ return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_7lengths___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1211 * :attr:`pysam.Samfile.references` * """ @@ -12764,7 +12024,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_ * t = [] */ -static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self) { PyObject *__pyx_v_t = NULL; long __pyx_v_x; PyObject *__pyx_r = NULL; @@ -12779,7 +12040,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 1211); /* "csamtools.pyx":1212 @@ -12789,7 +12050,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ * t = [] * for x from 0 <= x < self.samfile.header.n_targets: */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -12803,9 +12064,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1213 * def __get__(self): @@ -12815,7 +12076,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ * t.append( self.samfile.header.target_len[x] ) */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1213; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_t = __pyx_t_2; __pyx_t_2 = 0; @@ -12826,7 +12087,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ * t.append( self.samfile.header.target_len[x] ) * return tuple(t) */ - __pyx_t_5 = __pyx_v_self->samfile->header->n_targets; + __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets; for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) { /* "csamtools.pyx":1215 @@ -12836,7 +12097,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ * return tuple(t) * */ - __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((__pyx_v_self->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -12850,6 +12114,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ * property mapped: */ __Pyx_XDECREF(__pyx_r); + if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); @@ -12871,17 +12138,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_ return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_6mapped___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1221 * """total number of mapped reads in file. * """ @@ -12890,7 +12146,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) */ -static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self) { int __pyx_v_tid; uint32_t __pyx_v_total; PyObject *__pyx_r = NULL; @@ -12904,7 +12161,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9 const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 1221); /* "csamtools.pyx":1222 @@ -12914,7 +12171,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9 * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -12928,9 +12185,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9 __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1223 * def __get__(self): @@ -12939,16 +12196,16 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9 * * cdef int tid */ - __pyx_t_4 = (!__pyx_v_self->isbam); + __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam); if (__pyx_t_4) { __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_93), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":1226 * @@ -12966,7 +12223,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9 * total += pysam_get_mapped( self.index, tid ) * return total */ - __pyx_t_5 = __pyx_v_self->samfile->header->n_targets; + __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets; for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) { /* "csamtools.pyx":1228 @@ -12976,7 +12233,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9 * return total * */ - __pyx_v_total = (__pyx_v_total + pysam_get_mapped(__pyx_v_self->index, __pyx_v_tid)); + __pyx_v_total = (__pyx_v_total + pysam_get_mapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid)); } /* "csamtools.pyx":1229 @@ -13007,17 +12264,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9 return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_8unmapped___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1234 * """total number of unmapped reads in file. * """ @@ -13026,7 +12272,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) */ -static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self) { int __pyx_v_tid; uint32_t __pyx_v_total; PyObject *__pyx_r = NULL; @@ -13040,7 +12287,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 1234); /* "csamtools.pyx":1235 @@ -13050,7 +12297,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) * cdef int tid */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -13064,9 +12311,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1236 * def __get__(self): @@ -13075,16 +12322,16 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj * cdef int tid * cdef uint32_t total = 0 */ - __pyx_t_4 = (!__pyx_v_self->isbam); + __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam); if (__pyx_t_4) { __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_96), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":1238 * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) @@ -13102,7 +12349,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj * total += pysam_get_unmapped( self.index, tid ) * # get unmapped reads without coordinates */ - __pyx_t_5 = __pyx_v_self->samfile->header->n_targets; + __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets; for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) { /* "csamtools.pyx":1240 @@ -13112,7 +12359,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj * # get unmapped reads without coordinates * total += pysam_get_unmapped( self.index, -1 ) */ - __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, __pyx_v_tid)); + __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid)); } /* "csamtools.pyx":1242 @@ -13122,7 +12369,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj * return total * */ - __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, -1)); + __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, -1)); /* "csamtools.pyx":1243 * # get unmapped reads without coordinates @@ -13152,17 +12399,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_4text___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1247 * property text: * '''full contents of the :term:`sam file` header as a string.''' @@ -13171,7 +12407,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_s * return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text) */ -static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -13182,7 +12419,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 1247); /* "csamtools.pyx":1248 @@ -13192,7 +12429,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs * return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text) * */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -13206,9 +12443,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1249 * def __get__(self): @@ -13218,7 +12455,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs * property header: */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __pyx_f_9csamtools_from_string_and_size(__pyx_v_self->samfile->header->text, __pyx_v_self->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_from_string_and_size(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -13238,17 +12475,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_6header___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1255 * a two-level dictionary. * ''' @@ -13257,7 +12483,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v * */ -static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self) { PyObject *__pyx_v_result = NULL; PyObject *__pyx_v_t = NULL; PyObject *__pyx_v_line = NULL; @@ -13290,7 +12517,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 1255); /* "csamtools.pyx":1256 @@ -13300,7 +12527,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * * result = {} */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -13314,9 +12541,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1258 * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) @@ -13337,7 +12564,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * # convert to python string (note: call self.text to create 0-terminated string) * t = self.text */ - __pyx_t_4 = (__pyx_v_self->samfile->header->text != NULL); + __pyx_t_4 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text != NULL); if (__pyx_t_4) { /* "csamtools.pyx":1262 @@ -13347,7 +12574,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * for line in t.split("\n"): * if not line.strip(): continue */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_v_t = __pyx_t_2; __pyx_t_2 = 0; @@ -13374,10 +12601,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; for (;;) { - if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) { + if (PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break; __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; - } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) { + } else if (PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break; __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; } else { @@ -13411,10 +12638,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_3 = (!__pyx_t_4); if (__pyx_t_3) { - goto __pyx_L5_continue; - goto __pyx_L7; + goto __pyx_L7_continue; + goto __pyx_L9; } - __pyx_L7:; + __pyx_L9:; /* "csamtools.pyx":1265 * for line in t.split("\n"): @@ -13486,7 +12713,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (unlikely(!__pyx_t_3)) { __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_record); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_record); __Pyx_GIVEREF(__pyx_v_record); @@ -13519,15 +12746,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * result[record].append( "\t".join( fields[1:] ) ) * continue */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_3 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_3) { __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; - goto __pyx_L9; + goto __pyx_L11; } - __pyx_L9:; + __pyx_L11:; /* "csamtools.pyx":1273 * if record == "CO": @@ -13543,7 +12773,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8); __Pyx_GIVEREF(__pyx_t_8); __pyx_t_8 = 0; @@ -13564,10 +12794,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * * # the following is clumsy as generators do not work? */ - goto __pyx_L5_continue; - goto __pyx_L8; + goto __pyx_L7_continue; + goto __pyx_L10; } - __pyx_L8:; + __pyx_L10:; /* "csamtools.pyx":1277 * @@ -13601,10 +12831,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 } __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; for (;;) { - if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_8)) { + if (PyList_CheckExact(__pyx_t_8)) { if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_8)) break; __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; - } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) { + } else if (PyTuple_CheckExact(__pyx_t_8)) { if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_8)) break; __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; } else { @@ -13662,19 +12892,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_GOTREF(__pyx_t_12); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext; - index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L12_unpacking_failed; + index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L14_unpacking_failed; __Pyx_GOTREF(__pyx_t_9); - index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed; + index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L14_unpacking_failed; __Pyx_GOTREF(__pyx_t_1); if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; - goto __pyx_L13_unpacking_done; - __pyx_L12_unpacking_failed:; + goto __pyx_L15_unpacking_done; + __pyx_L14_unpacking_failed:; __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L13_unpacking_done:; + __pyx_L15_unpacking_done:; } __Pyx_XDECREF(__pyx_v_key); __pyx_v_key = __pyx_t_9; @@ -13715,7 +12945,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_INCREF(__pyx_v_value); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value); __Pyx_GIVEREF(__pyx_v_value); @@ -13725,7 +12955,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - goto __pyx_L14; + goto __pyx_L16; } /* "csamtools.pyx":1284 @@ -13753,7 +12983,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) ) */ if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L14; + goto __pyx_L16; } /*else*/ { @@ -13765,7 +12995,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * if VALID_HEADER_TYPES[record] == dict: */ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_INCREF(__pyx_v_key); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); @@ -13776,7 +13006,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_GOTREF(((PyObject *)__pyx_t_9)); __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_9)); __Pyx_GIVEREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; @@ -13787,7 +13017,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_L14:; + __pyx_L16:; } __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; @@ -13817,6 +13047,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * raise ValueError( "multiple '%s' lines are not permitted" % record ) * result[record] = x */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_4 = ((PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { @@ -13830,7 +13063,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_v_record); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; @@ -13840,9 +13073,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L16; + goto __pyx_L18; } - __pyx_L16:; + __pyx_L18:; /* "csamtools.pyx":1292 * if record in result: @@ -13852,7 +13085,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * if record not in result: result[record] = [] */ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L15; + goto __pyx_L17; } /* "csamtools.pyx":1293 @@ -13881,15 +13114,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * result[record].append( x ) * */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(((PyObject *)__pyx_t_8)); if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; - goto __pyx_L17; + goto __pyx_L19; } - __pyx_L17:; + __pyx_L19:; /* "csamtools.pyx":1295 * elif VALID_HEADER_TYPES[record] == list: @@ -13904,10 +13140,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; - goto __pyx_L15; + goto __pyx_L17; } - __pyx_L15:; - __pyx_L5_continue:; + __pyx_L17:; + __pyx_L7_continue:; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -13918,6 +13154,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * sq = [] * for ref, length in zip( self.references, self.lengths ): */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_4) { @@ -13929,7 +13168,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * sq.append( {'LN': length, 'SN': ref } ) */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_sq = __pyx_t_2; __pyx_t_2 = 0; @@ -13940,12 +13179,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * sq.append( {'LN': length, 'SN': ref } ) * result["SQ"] = sq */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(((PyObject *)__pyx_t_8)); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_9); @@ -13965,10 +13204,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 } __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; for (;;) { - if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_8)) { + if (PyList_CheckExact(__pyx_t_8)) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_8)) break; __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++; - } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_8)) { + } else if (PyTuple_CheckExact(__pyx_t_8)) { if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_8)) break; __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++; } else { @@ -14010,19 +13249,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_13 = Py_TYPE(__pyx_t_1)->tp_iternext; - index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L21_unpacking_failed; + index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L23_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L21_unpacking_failed; + index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L23_unpacking_failed; __Pyx_GOTREF(__pyx_t_7); if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_1), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - goto __pyx_L22_unpacking_done; - __pyx_L21_unpacking_failed:; + goto __pyx_L24_unpacking_done; + __pyx_L23_unpacking_failed:; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L22_unpacking_done:; + __pyx_L24_unpacking_done:; } __Pyx_XDECREF(__pyx_v_ref); __pyx_v_ref = __pyx_t_2; @@ -14038,6 +13277,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * result["SQ"] = sq * */ + if (unlikely(((PyObject *)__pyx_v_sq) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_9)); if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__LN), __pyx_v_length) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -14055,12 +13297,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 * return result */ if (PyDict_SetItem(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_sq)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L18; + goto __pyx_L20; } - __pyx_L18:; - goto __pyx_L4; + __pyx_L20:; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":1309 * result["SQ"] = sq @@ -14104,29 +13346,50 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9 return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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- PyObject *__pyx_r = 0; + PyObject *__pyx_v_line = NULL; + PyObject *__pyx_v_key = NULL; + PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("_buildLine (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + Py_ssize_t __pyx_t_5; + PyObject *(*__pyx_t_6)(PyObject *); + PyObject *__pyx_t_7 = NULL; + int __pyx_t_8; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("_buildLine"); + __Pyx_TraceCall("_buildLine", __pyx_f[0], 1311); { PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields); if (likely(values[0])) kw_args--; @@ -14139,7 +13402,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_sel } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -14158,38 +13421,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_sel __Pyx_RefNannyFinishContext(); 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_4 = PyList_Append(__pyx_v_line, __pyx_v_fields); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } /* "csamtools.pyx":1320 @@ -14253,7 +13487,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct * # defined tags */ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_fields); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields); __Pyx_GIVEREF(__pyx_v_fields); @@ -14270,10 +13504,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; for (;;) { - if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) { + if (PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break; __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; - } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) { + } else if (PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break; __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; } else { @@ -14298,10 +13532,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct * # defined tags * else: */ + if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; @@ -14309,7 +13546,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_INCREF(__pyx_v_key); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key); __Pyx_GIVEREF(__pyx_v_key); @@ -14323,7 +13560,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - goto __pyx_L3; + goto __pyx_L6; } /*else*/ { @@ -14349,10 +13586,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; for (;;) { - if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) { + if (PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break; __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; - } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) { + } else if (PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break; __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; } else { @@ -14387,10 +13624,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct * # write user fields * for key in fields: */ + if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; 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__pyx_t_5++; } else { @@ -14477,10 +13717,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct * * return "\t".join( line ) */ + if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = 0; @@ -14488,7 +13731,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __Pyx_GOTREF(__pyx_t_7); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_v_lines = __pyx_t_1; __pyx_t_1 = 0; @@ -14639,10 +13882,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; for (;;) { - if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) { + if (PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; - } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) { + } else if (PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; } else { @@ -14725,7 +13968,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 __pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); 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@@ -14771,10 +14014,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 * else: * for fields in new_header[record]: */ + if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __Pyx_INCREF(__pyx_v_data); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_data); __Pyx_GIVEREF(__pyx_v_data); @@ -14810,10 +14056,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 } __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; for (;;) { - if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_6)) { + if (PyList_CheckExact(__pyx_t_6)) { if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_6)) break; __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++; - } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_6)) { + } else if (PyTuple_CheckExact(__pyx_t_6)) { if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_6)) break; __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++; } else { @@ -14838,10 +14084,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 * * # then: user tags (lower case), sorted alphabetically */ + if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_fields); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields); __Pyx_GIVEREF(__pyx_v_fields); @@ -14877,7 +14126,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __pyx_t_6 = 0; @@ -14894,10 +14143,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 } __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; for (;;) { - if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) { + if (PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break; __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; - } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) { + } else if (PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break; __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; } else { @@ -14994,10 +14243,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 * else: * for fields in new_header[record]: */ + if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_data); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_data); __Pyx_GIVEREF(__pyx_v_data); @@ -15033,10 +14285,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 } __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; for (;;) { - if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) { + if (PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_1)) break; __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++; - } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) { + } else if (PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_1)) break; __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++; } else { @@ -15061,10 +14313,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 * * text = "\n".join(lines) + "\n" */ + if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __Pyx_INCREF(__pyx_v_fields); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields); __Pyx_GIVEREF(__pyx_v_fields); @@ -15095,7 +14350,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(((PyObject *)__pyx_v_lines)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_lines)); __Pyx_GIVEREF(((PyObject *)__pyx_v_lines)); @@ -15187,7 +14442,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 * try: */ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;} + } __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;} - __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2); @@ -15300,7 +14558,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 * dest.n_targets = len(seqs) */ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;} - __Pyx_GOTREF(__pyx_t_11); + __Pyx_GOTREF(((PyObject *)__pyx_t_11)); __Pyx_INCREF(__pyx_v_fields); PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_fields); __Pyx_GIVEREF(__pyx_v_fields); @@ -15311,7 +14569,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 __Pyx_GOTREF(((PyObject *)__pyx_t_11)); __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;} - __Pyx_GOTREF(__pyx_t_18); + __Pyx_GOTREF(((PyObject *)__pyx_t_18)); PyTuple_SET_ITEM(__pyx_t_18, 0, ((PyObject *)__pyx_t_11)); __Pyx_GIVEREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0; @@ -15349,6 +14607,9 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 * dest.target_name = calloc( dest.n_targets, sizeof(char*) ) * dest.target_len = calloc( dest.n_targets, sizeof(uint32_t) ) */ + if (unlikely(((PyObject *)__pyx_v_seqs) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs)); __pyx_v_dest->n_targets = __pyx_t_3; @@ -15528,17 +14789,6 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9 return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_40__iter__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1411 * ## Possible solutions: deprecate or open new file handle * ############################################################### @@ -15547,7 +14797,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self) * if not self.isbam and self.samfile.header.n_targets == 0: */ -static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -15559,7 +14810,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__iter__", 0); + __Pyx_RefNannySetupContext("__iter__"); __Pyx_TraceCall("__iter__", __pyx_f[0], 1411); /* "csamtools.pyx":1412 @@ -15569,7 +14820,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt * if not self.isbam and self.samfile.header.n_targets == 0: * raise NotImplementedError( "can not iterate over samfile without header") */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); 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if (__pyx_t_4) { - __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0); + __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0); __pyx_t_5 = __pyx_t_3; } else { __pyx_t_5 = __pyx_t_4; @@ -15615,9 +14866,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":1415 * if not self.isbam and self.samfile.header.n_targets == 0: @@ -15627,8 +14878,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt * cdef bam1_t * getCurrent( self ): */ __Pyx_XDECREF(__pyx_r); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - __pyx_r = ((PyObject *)__pyx_v_self); + __Pyx_INCREF(__pyx_v_self); + __pyx_r = __pyx_v_self; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -15657,7 +14908,7 @@ static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtool bam1_t *__pyx_r; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("getCurrent", 0); + __Pyx_RefNannySetupContext("getCurrent"); __Pyx_TraceCall("getCurrent", __pyx_f[0], 1417); /* "csamtools.pyx":1418 @@ -15689,7 +14940,7 @@ static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("cnext", 0); + __Pyx_RefNannySetupContext("cnext"); __Pyx_TraceCall("cnext", __pyx_f[0], 1420); /* "csamtools.pyx":1425 @@ -15709,19 +14960,6 @@ static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_9csamtools_7Samfile_42__next__[] = "\n python version of next().\n "; -struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile_42__next__; -static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_7Samfile_42__next__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":1427 * return samread(self.samfile, self.b) * @@ -15730,7 +14968,10 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self) * python version of next(). */ -static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self); /*proto*/ +static char __pyx_doc_9csamtools_7Samfile_21__next__[] = "\n python version of next().\n "; +struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile_21__next__; +static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self) { int __pyx_v_ret; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -15740,7 +14981,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__next__", 0); + __Pyx_RefNannySetupContext("__next__"); __Pyx_TraceCall("__next__", __pyx_f[0], 1427); /* "csamtools.pyx":1432 @@ -15750,7 +14991,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt * if (ret > 0): * return makeAlignedRead( self.b ) */ - __pyx_v_ret = samread(__pyx_v_self->samfile, __pyx_v_self->b); + __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b); /* "csamtools.pyx":1433 * cdef int ret @@ -15770,12 +15011,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt * raise StopIteration */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } /*else*/ { @@ -15789,7 +15030,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_L3:; + __pyx_L5:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -15804,24 +15045,42 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +/* "csamtools.pyx":1481 + * """ + * + * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<< + * + * if not samfile._isOpen(): + */ + +static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0; int __pyx_v_tid; int __pyx_v_beg; int __pyx_v_end; int __pyx_v_reopen; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0}; + PyObject *__pyx_v_mode = NULL; + PyObject *__pyx_v_store = NULL; int __pyx_r; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + char *__pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("__cinit__"); + __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481); { PyObject* values[5] = {0,0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4); case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); @@ -15831,7 +15090,7 @@ static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_ default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile); if (likely(values[0])) kw_args--; @@ -15861,19 +15120,7 @@ static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_ } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - } - if (values[4]) { - } else { - - /* "csamtools.pyx":1481 - * """ - * - * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<< - * - * if not samfile._isOpen(): - */ - __pyx_v_reopen = ((int)1); + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -15905,31 +15152,6 @@ static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_ return -1; __pyx_L4_argument_unpacking_done:; if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_beg, __pyx_v_end, __pyx_v_reopen); - goto __pyx_L0; - __pyx_L1_error:; - __pyx_r = -1; - __pyx_L0:; - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen) { - PyObject *__pyx_v_mode = NULL; - PyObject *__pyx_v_store = NULL; - int __pyx_r; - __Pyx_RefNannyDeclarations - PyObject *__pyx_t_1 = NULL; - PyObject *__pyx_t_2 = NULL; - int __pyx_t_3; - int __pyx_t_4; - char *__pyx_t_5; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__cinit__", 0); - __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481); /* "csamtools.pyx":1483 * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): @@ -15960,9 +15182,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":1486 * raise ValueError( "I/O operation on closed file" ) @@ -15993,9 +15215,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L7; } - __pyx_L4:; + __pyx_L7:; /* "csamtools.pyx":1491 * # makes sure that samfile stays alive as long as the @@ -16006,9 +15228,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c */ __Pyx_INCREF(((PyObject *)__pyx_v_samfile)); __Pyx_GIVEREF(((PyObject *)__pyx_v_samfile)); - __Pyx_GOTREF(__pyx_v_self->samfile); - __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile)); - __pyx_v_self->samfile = __pyx_v_samfile; + __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile); + __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile)); + ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile = __pyx_v_samfile; /* "csamtools.pyx":1493 * self.samfile = samfile @@ -16020,7 +15242,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c if (__pyx_v_samfile->isbam) { __Pyx_INCREF(((PyObject *)__pyx_n_b__rb)); __pyx_v_mode = __pyx_n_b__rb; - goto __pyx_L5; + goto __pyx_L8; } /*else*/ { @@ -16034,7 +15256,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c __Pyx_INCREF(((PyObject *)__pyx_n_b__r)); __pyx_v_mode = __pyx_n_b__r; } - __pyx_L5:; + __pyx_L8:; /* "csamtools.pyx":1498 * # reopen the file - note that this makes the iterator @@ -16068,7 +15290,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * assert self.fp != NULL */ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL); + ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL); /* "csamtools.pyx":1501 * store = StderrStore() @@ -16092,7 +15314,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * else: */ #ifndef CYTHON_WITHOUT_ASSERTIONS - if (unlikely(!(__pyx_v_self->fp != NULL))) { + if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp != NULL))) { PyErr_SetNone(PyExc_AssertionError); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } @@ -16105,8 +15327,8 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * else: * self.fp = self.samfile.samfile */ - __pyx_v_self->owns_samfile = 1; - goto __pyx_L6; + ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 1; + goto __pyx_L9; } /*else*/ { @@ -16117,7 +15339,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * self.owns_samfile = False * */ - __pyx_v_self->fp = __pyx_v_self->samfile->samfile; + ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->samfile; /* "csamtools.pyx":1506 * else: @@ -16126,9 +15348,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * * self.retval = 0 */ - __pyx_v_self->owns_samfile = 0; + ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 0; } - __pyx_L6:; + __pyx_L9:; /* "csamtools.pyx":1508 * self.owns_samfile = False @@ -16137,7 +15359,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * * self.iter = bam_iter_query(self.samfile.index, */ - __pyx_v_self->retval = 0; + ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval = 0; /* "csamtools.pyx":1510 * self.retval = 0 @@ -16146,7 +15368,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * tid, * beg, */ - __pyx_v_self->iter = bam_iter_query(__pyx_v_self->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end); + ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter = bam_iter_query(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end); /* "csamtools.pyx":1514 * beg, @@ -16155,7 +15377,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c * * def __iter__(self): */ - __pyx_v_self->b = bam_init1(); 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/*proto*/ +static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__iter__", 0); + __Pyx_RefNannySetupContext("__iter__"); __Pyx_TraceCall("__iter__", __pyx_f[0], 1516); /* "csamtools.pyx":1517 @@ -16206,8 +15418,8 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_ * cdef bam1_t * getCurrent( self ): */ __Pyx_XDECREF(__pyx_r); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - __pyx_r = ((PyObject *)__pyx_v_self); + __Pyx_INCREF(__pyx_v_self); + __pyx_r = __pyx_v_self; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -16230,7 +15442,7 @@ static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_ob bam1_t *__pyx_r; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("getCurrent", 0); + __Pyx_RefNannySetupContext("getCurrent"); __Pyx_TraceCall("getCurrent", __pyx_f[0], 1519); 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if (likely(values[0])) kw_args--; @@ -16455,19 +15667,7 @@ static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_sel } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - } - if (values[1]) { - } else { - - /* "csamtools.pyx":1550 - * """ - * - * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<< - * - * if not samfile._isOpen(): - */ - __pyx_v_reopen = ((int)1); + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -16493,31 +15693,6 @@ static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_sel return -1; 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__pyx_v_mode = __pyx_n_b__r; } - __pyx_L4:; + __pyx_L7:; /* "csamtools.pyx":1559 * @@ -16610,7 +15785,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam * assert self.fp != NULL */ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL); + ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL); /* "csamtools.pyx":1562 * store = StderrStore() @@ -16634,7 +15809,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam * else: */ #ifndef CYTHON_WITHOUT_ASSERTIONS - if (unlikely(!(__pyx_v_self->fp != NULL))) { + if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp != NULL))) { PyErr_SetNone(PyExc_AssertionError); {__pyx_filename = __pyx_f[0]; 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/*proto*/ +static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__iter__", 0); + __Pyx_RefNannySetupContext("__iter__"); __Pyx_TraceCall("__iter__", __pyx_f[0], 1572); /* "csamtools.pyx":1573 @@ -16730,8 +15895,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj * cdef bam1_t * getCurrent( self ): */ __Pyx_XDECREF(__pyx_r); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - __pyx_r = ((PyObject *)__pyx_v_self); + __Pyx_INCREF(__pyx_v_self); + __pyx_r = __pyx_v_self; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -16754,7 +15919,7 @@ static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9 bam1_t *__pyx_r; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("getCurrent", 0); + __Pyx_RefNannySetupContext("getCurrent"); __Pyx_TraceCall("getCurrent", __pyx_f[0], 1575); 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int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__next__", 0); + __Pyx_RefNannySetupContext("__next__"); __Pyx_TraceCall("__next__", __pyx_f[0], 1582); /* "csamtools.pyx":1588 @@ -16847,7 +16002,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj * if (ret > 0): * return makeAlignedRead( self.b ) */ - __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_self->b); + __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp, ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b); /* "csamtools.pyx":1589 * cdef int ret @@ -16867,12 +16022,12 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj * raise StopIteration */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b); 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/*proto*/ +static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__iter__", 0); + __Pyx_RefNannySetupContext("__iter__"); __Pyx_TraceCall("__iter__", __pyx_f[0], 1611); /* "csamtools.pyx":1612 @@ -17218,8 +16330,8 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx * def __next__(self): */ __Pyx_XDECREF(__pyx_r); - __Pyx_INCREF(((PyObject *)__pyx_v_self)); - __pyx_r = ((PyObject *)__pyx_v_self); + __Pyx_INCREF(__pyx_v_self); + __pyx_r = __pyx_v_self; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -17230,19 +16342,6 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n "; 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+struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__; +static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -17263,7 +16365,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__next__", 0); + __Pyx_RefNannySetupContext("__next__"); __Pyx_TraceCall("__next__", __pyx_f[0], 1614); /* "csamtools.pyx":1620 @@ -17273,7 +16375,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx * if not self.samfile.nreferences: * raise StopIteration */ - __pyx_t_1 = (__pyx_v_self->tid == -1); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid == -1); if (__pyx_t_1) { /* "csamtools.pyx":1621 @@ -17283,7 +16385,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx * raise StopIteration * self.tid = 0 */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -17299,9 +16401,9 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1622; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":1623 * if not self.samfile.nreferences: @@ -17310,7 +16412,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx * self.nextiter() * */ - __pyx_v_self->tid = 0; 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} - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":1626 * self.nextiter() @@ -17346,7 +16448,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx * * # If current iterator is not exhausted, return aligned read */ - ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)__pyx_v_self->rowiter->__pyx_vtab)->cnext(__pyx_v_self->rowiter); + ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter); /* "csamtools.pyx":1630 * @@ -17355,7 +16457,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx * return makeAlignedRead(self.rowiter.b) * */ - __pyx_t_3 = (__pyx_v_self->rowiter->retval > 0); + __pyx_t_3 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->retval > 0); if (__pyx_t_3) { /* "csamtools.pyx":1631 @@ -17366,14 +16468,14 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx * self.tid += 1 */ __Pyx_XDECREF(__pyx_r); 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/* "csamtools.pyx":1636 * @@ -17391,9 +16493,9 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx * self.nextiter() * else: */ - __pyx_t_4 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; 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/*proto*/ +static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0; PyObject *__pyx_v_positions = 0; int __pyx_v_reopen; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0}; + PyObject *__pyx_v_mode = NULL; + PyObject *__pyx_v_store = NULL; int __pyx_r; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_t_3; + int __pyx_t_4; + char *__pyx_t_5; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("__cinit__"); + __Pyx_TraceCall("__cinit__", __pyx_f[0], 1647); { PyObject* values[3] = {0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -17471,7 +16591,7 @@ static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile); if (likely(values[0])) kw_args--; @@ -17489,19 +16609,7 @@ static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - } - if (values[2]) { - } else { - - /* "csamtools.pyx":1647 - * """ - * - * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<< - * - * if not samfile._isOpen(): - */ - __pyx_v_reopen = ((int)1); 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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L7; } - __pyx_L4:; + __pyx_L7:; /* "csamtools.pyx":1655 * raise ValueError( "I/O operation on closed file" ) @@ -17677,7 +16760,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj * assert self.fp != NULL */ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL); + ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL); /* "csamtools.pyx":1662 * store = StderrStore() @@ -17701,7 +16784,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj * else: */ #ifndef CYTHON_WITHOUT_ASSERTIONS - if (unlikely(!(__pyx_v_self->fp != NULL))) { + if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp != NULL))) { PyErr_SetNone(PyExc_AssertionError); 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/*proto*/ +static char __pyx_doc_9csamtools_14IteratorColumn_3hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference"; +static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("hasReference", 0); + __Pyx_RefNannySetupContext("hasReference"); __Pyx_TraceCall("hasReference", __pyx_f[0], 1858); /* "csamtools.pyx":1861 @@ -19003,8 +18019,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx * cdef setMask( self, mask ): */ __Pyx_XDECREF(__pyx_r); - __Pyx_INCREF(((PyObject *)__pyx_v_self->fastafile)); - __pyx_r = ((PyObject *)__pyx_v_self->fastafile); + __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile)); + __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile); 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -19747,7 +18723,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj * self.end = end * self.truncate = truncate */ - __pyx_v_self->start = __pyx_v_start; + ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start = __pyx_v_start; /* "csamtools.pyx":1944 * self.setupIteratorData( tid, start, end, 1 ) @@ -19756,7 +18732,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj * self.truncate = truncate * */ - __pyx_v_self->end = __pyx_v_end; + ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->end = __pyx_v_end; /* "csamtools.pyx":1945 * self.start = start @@ -19765,7 +18741,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj * * def __next__(self): */ - __pyx_v_self->truncate = __pyx_v_truncate; + ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate = __pyx_v_truncate; __pyx_r = 0; goto __pyx_L0; @@ -19774,24 +18750,12 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; + __Pyx_XDECREF(__pyx_v_kwargs); __Pyx_TraceReturn(Py_None); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self); /*proto*/ -static char __pyx_doc_9csamtools_20IteratorColumnRegion_2__next__[] = "python version of next().\n "; -struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__; -static PyObject *__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__next__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)); 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+ __Pyx_RefNannySetupContext("__next__"); __Pyx_TraceCall("__next__", __pyx_f[0], 1947); /* "csamtools.pyx":1951 @@ -19829,7 +18796,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p * if self.n_plp < 0: * raise ValueError("error during iteration" ) */ - ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)); + ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)); /* "csamtools.pyx":1953 * while 1: @@ -19838,7 +18805,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p * raise ValueError("error during iteration" ) * */ - __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp < 0); if (__pyx_t_1) { /* "csamtools.pyx":1954 @@ -19853,9 +18820,9 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + goto __pyx_L7; } - __pyx_L5:; + __pyx_L7:; /* "csamtools.pyx":1956 * raise ValueError("error during iteration" ) @@ -19864,7 +18831,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p * raise StopIteration * */ - __pyx_t_1 = (__pyx_v_self->__pyx_base.plp == NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp == NULL); if (__pyx_t_1) { /* "csamtools.pyx":1957 @@ -19876,9 +18843,9 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1957; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L6; + goto __pyx_L8; } - __pyx_L6:; + __pyx_L8:; /* "csamtools.pyx":1959 * raise StopIteration @@ -19887,7 +18854,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p * if self.start < self.pos: continue * if self.pos >= self.end: raise StopIteration */ - if (__pyx_v_self->truncate) { + if (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate) { /* "csamtools.pyx":1960 * @@ -19896,12 +18863,12 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p * if self.pos >= self.end: raise StopIteration * */ - __pyx_t_1 = (__pyx_v_self->start < __pyx_v_self->__pyx_base.pos); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start < ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos); if (__pyx_t_1) { - goto __pyx_L3_continue; - goto __pyx_L8; + goto __pyx_L5_continue; + goto __pyx_L10; } - __pyx_L8:; + __pyx_L10:; 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if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0; - __pyx_L3_continue:; + __pyx_L5_continue:; } __pyx_r = Py_None; __Pyx_INCREF(Py_None); @@ -19958,36 +18925,51 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":1980 * @@ -20066,7 +19017,7 @@ static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_ob */ __pyx_t_4.__pyx_n = 1; __pyx_t_4.reopen = 1; - __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1980; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); 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int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__next__", 0); + __Pyx_RefNannySetupContext("__next__"); __Pyx_TraceCall("__next__", __pyx_f[0], 1982); /* "csamtools.pyx":1986 @@ -20135,7 +19077,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __ * * if self.n_plp < 0: */ - ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)); + ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)); /* "csamtools.pyx":1989 * self.cnext() @@ -20144,7 +19086,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __ * raise ValueError("error during iteration" ) * */ - __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp < 0); if (__pyx_t_1) { /* "csamtools.pyx":1990 @@ -20159,9 +19101,9 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __ __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + goto __pyx_L7; } - __pyx_L5:; + __pyx_L7:; /* "csamtools.pyx":1993 * @@ -20170,7 +19112,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __ * return makePileupProxy( &self.plp, * self.tid, */ - __pyx_t_1 = (__pyx_v_self->__pyx_base.plp != NULL); + __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp != NULL); if (__pyx_t_1) { /* "csamtools.pyx":1994 @@ -20189,14 +19131,14 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __ * * # otherwise, proceed to next reference or stop */ - __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0; - goto __pyx_L6; + goto __pyx_L8; } - __pyx_L6:; + __pyx_L8:; /* "csamtools.pyx":2000 * @@ -20205,7 +19147,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __ * if self.tid < self.samfile.nreferences: * self.setupIteratorData( self.tid, 0, max_pos, 0 ) */ - __pyx_v_self->__pyx_base.tid = (__pyx_v_self->__pyx_base.tid + 1); 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__pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_v_seq = __pyx_t_2; __pyx_t_2 = 0; @@ -21107,11 +20021,11 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * else: * seq = self.seq.decode('ascii') */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_v_qual = __pyx_t_2; __pyx_t_2 = 0; - goto __pyx_L3; + goto __pyx_L5; } /*else*/ { @@ -21122,7 +20036,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * qual = self.qual.decode('ascii') * return "\t".join(map(str, (self.qname, */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -21140,7 +20054,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * return "\t".join(map(str, (self.qname, * self.flag, */ - __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -21151,7 +20065,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs __pyx_v_qual = __pyx_t_2; __pyx_t_2 = 0; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2155 * seq = self.seq.decode('ascii') @@ -21163,7 +20077,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_r); __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); /* "csamtools.pyx":2156 @@ -21173,7 +20087,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * self.rname, * self.pos, */ - __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); /* "csamtools.pyx":2157 @@ -21183,7 +20097,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * self.pos, * self.mapq, */ - __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); /* "csamtools.pyx":2158 @@ -21193,7 +20107,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * self.mapq, * self.cigar, */ - __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); /* "csamtools.pyx":2159 @@ -21203,7 +20117,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * self.cigar, * self.mrnm, */ - __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); /* "csamtools.pyx":2160 @@ -21213,7 +20127,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * self.mrnm, * self.mpos, */ - __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); /* "csamtools.pyx":2161 @@ -21223,7 +20137,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * self.mpos, * self.rlen, */ - __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); /* "csamtools.pyx":2162 @@ -21233,7 +20147,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * self.rlen, * seq, */ - __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); /* "csamtools.pyx":2163 @@ -21243,7 +20157,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * seq, * qual, */ - __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_11); /* "csamtools.pyx":2166 @@ -21253,10 +20167,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs * * def compare(self, AlignedRead other): */ - __pyx_t_12 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_12); __pyx_t_13 = PyTuple_New(12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_13); + __Pyx_GOTREF(((PyObject *)__pyx_t_13)); PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_4); @@ -21294,7 +20208,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs __pyx_t_11 = 0; __pyx_t_12 = 0; __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_12); + __Pyx_GOTREF(((PyObject *)__pyx_t_12)); __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type)))); PyTuple_SET_ITEM(__pyx_t_12, 0, ((PyObject *)((PyObject*)(&PyString_Type)))); __Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type)))); @@ -21305,7 +20219,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs __Pyx_GOTREF(__pyx_t_13); __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0; __pyx_t_12 = PyTuple_New(1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_12); + __Pyx_GOTREF(((PyObject *)__pyx_t_12)); PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_13); __Pyx_GIVEREF(__pyx_t_13); __pyx_t_13 = 0; @@ -21343,23 +20257,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/ -static char __pyx_doc_9csamtools_11AlignedRead_6compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*"; -static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("compare (wrapper)", 0); - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_6compare(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_other)); - goto __pyx_L0; - __pyx_L1_error:; - __pyx_r = NULL; - __pyx_L0:; - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2168 * self.tags ))) * @@ -21368,7 +20265,9 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_se * */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_other) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/ +static char __pyx_doc_9csamtools_11AlignedRead_3compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*"; +static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) { int __pyx_v_retval; bam1_t *__pyx_v_t; bam1_t *__pyx_v_o; @@ -21380,8 +20279,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("compare", 0); + __Pyx_RefNannySetupContext("compare"); __Pyx_TraceCall("compare", __pyx_f[0], 2168); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":2174 * cdef bam1_t *t, *o @@ -21390,7 +20290,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs * o = other._delegate * */ - __pyx_v_t = __pyx_v_self->_delegate; + __pyx_v_t = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2175 * @@ -21399,7 +20299,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs * * # uncomment for debugging purposes */ - __pyx_v_o = __pyx_v_other->_delegate; 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/*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self) { bam1_t *__pyx_v_src; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -21580,7 +20460,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2203); /* "csamtools.pyx":2205 @@ -21590,7 +20470,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o * if src.core.l_qname == 0: return None * return _charptr_to_str(bam1_qname( src )) */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2206 * cdef bam1_t * src @@ -21605,9 +20485,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2207 * src = self._delegate @@ -21636,17 +20516,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qname)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2209 * return _charptr_to_str(bam1_qname( src )) * @@ -21655,7 +20524,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_s * qname = _force_bytes(qname) */ -static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname) { +static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) { bam1_t *__pyx_v_src; int __pyx_v_l; char *__pyx_v_p; @@ -21671,7 +20541,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9c const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2209); __Pyx_INCREF(__pyx_v_qname); @@ -21696,9 +20566,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9c if (__pyx_t_5) { __pyx_r = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2211 * def __set__(self, qname ): @@ -21720,7 +20590,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9c * p = bam1_qname( src ) * */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; 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/*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self) { uint32_t *__pyx_v_cigar_p; bam1_t *__pyx_v_src; PyObject *__pyx_v_op = 0; @@ -21827,7 +20687,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2259); /* "csamtools.pyx":2265 @@ -21837,7 +20697,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o * if src.core.n_cigar == 0: return None * */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2266 * @@ -21852,9 +20712,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2268 * if src.core.n_cigar == 0: return None @@ -21864,7 +20724,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o * for k from 0 <= k < src.core.n_cigar: */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2268; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_cigar = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; @@ -21921,7 +20781,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o * */ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_INCREF(__pyx_v_op); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_op); __Pyx_GIVEREF(__pyx_v_op); @@ -21963,17 +20823,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_values)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2276 * return cigar * @@ -21982,7 +20831,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_s * cdef uint32_t * p */ -static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values) { +static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) { uint32_t *__pyx_v_p; bam1_t *__pyx_v_src; PyObject *__pyx_v_op = 0; @@ -22006,7 +20856,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2276); /* "csamtools.pyx":2277 @@ -22030,9 +20880,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c if (__pyx_t_5) { __pyx_r = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2283 * cdef int k @@ -22050,7 +20900,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c * * # get location of cigar string */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2288 * @@ -22114,10 +20964,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c __pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext; } for (;;) { - if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) { + if (PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break; __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; - } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) { + } else if (PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break; __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; } else { @@ -22159,19 +21009,19 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext; - index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed; + index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_8); - index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed; + index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_9); if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - goto __pyx_L7_unpacking_done; - __pyx_L6_unpacking_failed:; + goto __pyx_L9_unpacking_done; + __pyx_L8_unpacking_failed:; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L7_unpacking_done:; + __pyx_L9_unpacking_done:; } __Pyx_XDECREF(__pyx_v_op); __pyx_v_op = __pyx_t_8; @@ -22234,17 +21084,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2316 * Returns the empty string if not present. * ''' @@ -22253,7 +21092,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObje * if c == None: return "" */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self) { PyObject *__pyx_v_c = NULL; PyObject *__pyx_v_x = NULL; PyObject *__pyx_v_y = NULL; @@ -22275,7 +21115,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2316); /* "csamtools.pyx":2317 @@ -22285,7 +21125,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct * if c == None: return "" * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c]) */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_c = __pyx_t_1; __pyx_t_1 = 0; @@ -22306,7 +21146,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __Pyx_INCREF(((PyObject *)__pyx_kp_s_16)); __pyx_r = ((PyObject *)__pyx_kp_s_16); goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } /*else*/ { @@ -22321,7 +21161,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); if (PyList_CheckExact(__pyx_v_c) || PyTuple_CheckExact(__pyx_v_c)) { __pyx_t_4 = __pyx_v_c; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0; __pyx_t_6 = NULL; @@ -22331,10 +21171,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext; } for (;;) { - if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) { + if (PyList_CheckExact(__pyx_t_4)) { if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break; __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; - } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) { + } else if (PyTuple_CheckExact(__pyx_t_4)) { if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break; __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; } else { @@ -22376,19 +21216,19 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext; - index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed; + index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_8); - index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed; + index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_9); if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - goto __pyx_L7_unpacking_done; - __pyx_L6_unpacking_failed:; + goto __pyx_L9_unpacking_done; + __pyx_L8_unpacking_failed:; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L7_unpacking_done:; + __pyx_L9_unpacking_done:; } __Pyx_XDECREF(__pyx_v_x); __pyx_v_x = __pyx_t_8; @@ -22400,7 +21240,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_t_7 = PyInt_FromLong((__pyx_v_9csamtools_CODE2CIGAR[__pyx_t_12])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __Pyx_INCREF(__pyx_v_y); @@ -22415,7 +21255,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct } __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __Pyx_GOTREF(((PyObject *)__pyx_t_4)); __Pyx_INCREF(((PyObject *)__pyx_t_3)); PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3)); __Pyx_GIVEREF(((PyObject *)__pyx_t_3)); @@ -22428,7 +21268,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_t_3 = 0; goto __pyx_L0; } - __pyx_L3:; + __pyx_L5:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -22452,17 +21292,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_cigar)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2321 * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c]) * @@ -22471,7 +21300,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__ * parts = CIGAR_REGEX.findall( cigar ) */ -static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar) { +static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) { PyObject *__pyx_v_parts = NULL; PyObject *__pyx_v_x = NULL; PyObject *__pyx_v_y = NULL; @@ -22493,7 +21323,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2321); /* "csamtools.pyx":2322 @@ -22516,12 +21346,12 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx } if (__pyx_t_5) { __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); + if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2323 * def __set__(self, cigar): @@ -22536,7 +21366,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_cigar); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_cigar); __Pyx_GIVEREF(__pyx_v_cigar); @@ -22555,7 +21385,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx * property seq: */ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); if (PyList_CheckExact(__pyx_v_parts) || PyTuple_CheckExact(__pyx_v_parts)) { __pyx_t_1 = __pyx_v_parts; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0; __pyx_t_8 = NULL; @@ -22565,10 +21395,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx __pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext; } for (;;) { - if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) { + if (PyList_CheckExact(__pyx_t_1)) { if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break; __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; - } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) { + } else if (PyTuple_CheckExact(__pyx_t_1)) { if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break; __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; } else { @@ -22610,19 +21440,19 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx __Pyx_GOTREF(__pyx_t_11); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext; - index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed; + index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_9); - index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L6_unpacking_failed; + index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_10); if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - goto __pyx_L7_unpacking_done; - __pyx_L6_unpacking_failed:; + goto __pyx_L9_unpacking_done; + __pyx_L8_unpacking_failed:; __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L7_unpacking_done:; + __pyx_L9_unpacking_done:; } __Pyx_XDECREF(__pyx_v_x); __pyx_v_x = __pyx_t_9; @@ -22633,7 +21463,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR2CODE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_GOTREF(((PyObject *)__pyx_t_10)); __Pyx_INCREF(__pyx_v_x); PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_x); __Pyx_GIVEREF(__pyx_v_x); @@ -22645,7 +21475,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); __Pyx_INCREF(__pyx_v_y); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_y); __Pyx_GIVEREF(__pyx_v_y); @@ -22653,7 +21483,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10); __Pyx_GIVEREF(__pyx_t_10); PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_6); @@ -22664,7 +21494,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_r = 0; @@ -22687,17 +21517,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; 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int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2330); /* "csamtools.pyx":2333 @@ -22726,7 +21546,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj * * if src.core.l_qseq == 0: return None */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2335 * src = self._delegate @@ -22741,9 +21561,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2337 * if src.core.l_qseq == 0: return None @@ -22772,17 +21592,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_seq)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2339 * return get_seq_range(src, 0, src.core.l_qseq) * @@ -22791,7 +21600,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_sel * # if no quality information is present, the first byte says 0xff. */ -static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq) { +static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) { bam1_t *__pyx_v_src; uint8_t *__pyx_v_p; char *__pyx_v_s; @@ -22813,7 +21623,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2339); __Pyx_INCREF(__pyx_v_seq); @@ -22838,9 +21648,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa if (__pyx_t_5) { __pyx_r = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2344 * @@ -22862,7 +21672,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa * * l = len(seq) */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2352 * src = self._delegate @@ -23002,17 +21812,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qual___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2384 * * In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.""" @@ -23021,7 +21820,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__py * cdef bam1_t * src */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self) { bam1_t *__pyx_v_src; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -23031,7 +21831,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2384); /* "csamtools.pyx":2389 @@ -23041,7 +21841,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob * * if src.core.l_qseq == 0: return None */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2391 * src = self._delegate @@ -23056,9 +21856,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2393 * if src.core.l_qseq == 0: return None @@ -23087,17 +21887,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2395 * return get_qual_range(src, 0, src.core.l_qseq) * @@ -23106,7 +21895,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_se * cdef bam1_t * src */ -static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) { +static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) { bam1_t *__pyx_v_src; uint8_t *__pyx_v_p; char *__pyx_v_q; @@ -23127,7 +21917,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2395); __Pyx_INCREF(__pyx_v_qual); @@ -23138,7 +21928,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs * p = bam1_qual( src ) * if qual == None or len(qual) == 0: */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2403 * @@ -23187,9 +21977,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs */ __pyx_r = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2408 * p[0] = 0xff @@ -23246,7 +22036,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs __pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(((PyObject *)__pyx_t_8)); PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7); @@ -23257,7 +22047,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_8); + __Pyx_GOTREF(((PyObject *)__pyx_t_8)); PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7)); __Pyx_GIVEREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; @@ -23267,9 +22057,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L4; + goto __pyx_L6; } - __pyx_L4:; + __pyx_L6:; /* "csamtools.pyx":2415 * if src.core.l_qseq != l: @@ -23320,17 +22110,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5query___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2431 * were not considered for alignment may have been retained.""" * @@ -23339,7 +22118,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__p * cdef uint32_t start, end */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self) { bam1_t *__pyx_v_src; uint32_t __pyx_v_start; uint32_t __pyx_v_end; @@ -23352,7 +22132,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2431); /* "csamtools.pyx":2436 @@ -23362,7 +22142,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o * * if src.core.l_qseq == 0: return None */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2438 * src = self._delegate @@ -23377,9 +22157,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2440 * if src.core.l_qseq == 0: return None @@ -23428,17 +22208,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self); 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/*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int32_t __pyx_t_1; @@ -23623,7 +22373,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_ob const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2469); /* "csamtools.pyx":2470 @@ -23634,7 +22384,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_ob * property qlen: */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_f_9csamtools_query_end(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_f_9csamtools_query_end(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; @@ -23654,17 +22404,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_ob return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2474 * property qlen: * """Length of the aligned query sequence""" @@ -23673,7 +22412,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__py * src = self._delegate */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self) { bam1_t *__pyx_v_src; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -23684,7 +22424,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_ob const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2474); /* "csamtools.pyx":2476 @@ -23694,7 +22434,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_ob * return query_end(src)-query_start(src) * */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2477 * cdef bam1_t * src @@ -23725,17 +22465,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_ob return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tags___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2494 * multiple times. * """ @@ -23744,7 +22473,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__py * cdef bam1_t * src */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self) { bam1_t *__pyx_v_src; uint8_t *__pyx_v_s; char __pyx_v_auxtag[3]; @@ -23773,7 +22503,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2494); /* "csamtools.pyx":2503 @@ -23783,7 +22513,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * if src.l_aux == 0: return [] * s = bam1_aux( src ) */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2504 * @@ -23796,13 +22526,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob if (__pyx_t_1) { __Pyx_XDECREF(__pyx_r); __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2504; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2505 * src = self._delegate @@ -23821,7 +22551,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * while s < (src.data + src.data_len): */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_result = __pyx_t_2; __pyx_t_2 = 0; @@ -23920,7 +22650,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * value = bam_aux2i(s) */ __pyx_v_s = (__pyx_v_s + 1); - goto __pyx_L6; + goto __pyx_L8; } /* "csamtools.pyx":2517 @@ -23962,7 +22692,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * value = bam_aux2i(s) */ __pyx_v_s = (__pyx_v_s + 2); - goto __pyx_L6; + goto __pyx_L8; } /* "csamtools.pyx":2520 @@ -24004,7 +22734,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * value = bam_aux2f(s) */ __pyx_v_s = (__pyx_v_s + 4); - goto __pyx_L6; + goto __pyx_L8; } /* "csamtools.pyx":2523 @@ -24038,7 +22768,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * value = bam_aux2d(s) */ __pyx_v_s = (__pyx_v_s + 4); - goto __pyx_L6; + goto __pyx_L8; } /* "csamtools.pyx":2526 @@ -24072,7 +22802,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * value = "%c" % bam_aux2A(s) */ __pyx_v_s = (__pyx_v_s + 8); - goto __pyx_L6; + goto __pyx_L8; } /* "csamtools.pyx":2529 @@ -24109,7 +22839,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * value = _charptr_to_str(bam_aux2Z(s)) */ __pyx_v_s = (__pyx_v_s + 1); - goto __pyx_L6; + goto __pyx_L8; } /* "csamtools.pyx":2532 @@ -24152,7 +22882,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob */ __pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2535; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_s = (__pyx_v_s + (__pyx_t_7 + 1)); - goto __pyx_L6; + goto __pyx_L8; } /* "csamtools.pyx":2536 @@ -24214,21 +22944,21 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob __Pyx_GOTREF(__pyx_t_10); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext; - index = 0; __pyx_t_2 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed; + index = 0; __pyx_t_2 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L9_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - index = 1; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L7_unpacking_failed; + index = 1; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L9_unpacking_failed; __Pyx_GOTREF(__pyx_t_8); - index = 2; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed; + index = 2; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L9_unpacking_failed; __Pyx_GOTREF(__pyx_t_9); if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; - goto __pyx_L8_unpacking_done; - __pyx_L7_unpacking_failed:; + goto __pyx_L10_unpacking_done; + __pyx_L9_unpacking_failed:; __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L8_unpacking_done:; + __pyx_L10_unpacking_done:; } __pyx_t_12 = __Pyx_PyInt_from_py_uint8_t(__pyx_t_2); if (unlikely((__pyx_t_12 == (uint8_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -24248,9 +22978,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * s += 1 */ __pyx_v_s = (__pyx_v_s + ((5 + (__pyx_v_nvalues * __pyx_v_byte_size)) - 1)); - goto __pyx_L6; + goto __pyx_L8; } - __pyx_L6:; + __pyx_L8:; /* "csamtools.pyx":2542 * s += 5 + ( nvalues * byte_size) - 1 @@ -24268,11 +22998,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob * * return result */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); - if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_9); + if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __Pyx_INCREF(__pyx_v_value); @@ -24314,17 +23046,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tags)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2548 * return result * @@ -24333,7 +23054,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_se * cdef uint8_t * s */ -static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags) { +static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) { bam1_t *__pyx_v_src; uint8_t *__pyx_v_s; char *__pyx_v_temp; @@ -24375,7 +23097,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2548); /* "csamtools.pyx":2554 @@ -24385,7 +23107,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs * * fmts, args = ["<"], [] */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2556 * src = self._delegate @@ -24395,12 +23117,12 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs * if tags != None: */ __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_138)); PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_138)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_138)); __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_fmts = __pyx_t_1; __pyx_t_1 = 0; __pyx_v_args = __pyx_t_2; @@ -24435,10 +23157,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_5 = Py_TYPE(__pyx_t_2)->tp_iternext; } for (;;) { - if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_2)) { + if (PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break; __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; - } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_2)) { + } else if (PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break; __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; } else { @@ -24480,19 +23202,19 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext; - index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L6_unpacking_failed; + index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_6); - index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L6_unpacking_failed; + index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_7); if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - goto __pyx_L7_unpacking_done; - __pyx_L6_unpacking_failed:; + goto __pyx_L9_unpacking_done; + __pyx_L8_unpacking_failed:; __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L7_unpacking_done:; + __pyx_L9_unpacking_done:; } __Pyx_XDECREF(__pyx_v_pytag); __pyx_v_pytag = __pyx_t_6; @@ -24527,9 +23249,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_DECREF(__pyx_v_pytag); __pyx_v_pytag = __pyx_t_7; __pyx_t_7 = 0; - goto __pyx_L8; + goto __pyx_L10; } - __pyx_L8:; + __pyx_L10:; /* "csamtools.pyx":2564 * if not type(pytag) is bytes: @@ -24599,7 +23321,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_datatype); __pyx_v_datatype = __pyx_t_1; __pyx_t_1 = 0; - goto __pyx_L10; + goto __pyx_L12; } /*else*/ { @@ -24611,7 +23333,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs * # signed ints */ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_value); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value); __Pyx_GIVEREF(__pyx_v_value); @@ -24619,7 +23341,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_value); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value); __Pyx_GIVEREF(__pyx_v_value); @@ -24697,7 +23419,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_datatype); __pyx_v_datatype = __pyx_t_6; __pyx_t_6 = 0; - goto __pyx_L12; + goto __pyx_L14; } /* "csamtools.pyx":2578 @@ -24722,7 +23444,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_datatype); __pyx_v_datatype = __pyx_t_1; __pyx_t_1 = 0; - goto __pyx_L12; + goto __pyx_L14; } /* "csamtools.pyx":2579 @@ -24740,7 +23462,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -24750,7 +23472,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L12; + goto __pyx_L14; } /*else*/ { @@ -24772,8 +23494,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_v_datatype = __pyx_t_6; __pyx_t_6 = 0; } - __pyx_L12:; - goto __pyx_L11; + __pyx_L14:; + goto __pyx_L13; } /*else*/ { @@ -24799,7 +23521,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_datatype); __pyx_v_datatype = __pyx_t_1; __pyx_t_1 = 0; - goto __pyx_L13; + goto __pyx_L15; } /* "csamtools.pyx":2585 @@ -24824,7 +23546,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_datatype); __pyx_v_datatype = __pyx_t_6; __pyx_t_6 = 0; - goto __pyx_L13; + goto __pyx_L15; } /* "csamtools.pyx":2586 @@ -24842,7 +23564,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6)); __Pyx_GIVEREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; @@ -24852,7 +23574,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_Raise(__pyx_t_6, 0, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L13; + goto __pyx_L15; } /*else*/ { @@ -24874,11 +23596,11 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_v_datatype = __pyx_t_1; __pyx_t_1 = 0; } - __pyx_L13:; + __pyx_L15:; } - __pyx_L11:; + __pyx_L13:; } - __pyx_L10:; + __pyx_L12:; /* "csamtools.pyx":2589 * else: datafmt, datatype = "I", 'I' @@ -24891,7 +23613,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_datafmt); @@ -24962,7 +23684,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); __pyx_t_14 = PyList_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); + __Pyx_GOTREF(((PyObject *)__pyx_t_14)); PyList_SET_ITEM(__pyx_t_14, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); PyList_SET_ITEM(__pyx_t_14, 1, __pyx_t_8); @@ -24976,7 +23698,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_13 = 0; __pyx_t_7 = 0; __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __Pyx_INCREF(__pyx_v_value); PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value); __Pyx_GIVEREF(__pyx_v_value); @@ -24988,7 +23710,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0; __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_13); + __Pyx_GOTREF(((PyObject *)__pyx_t_13)); PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7)); __Pyx_GIVEREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; @@ -25005,6 +23727,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs * continue * */ + if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_datafmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":2595 @@ -25014,10 +23739,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs * * if t is float: */ - goto __pyx_L4_continue; - goto __pyx_L9; + goto __pyx_L6_continue; + goto __pyx_L11; } - __pyx_L9:; + __pyx_L11:; /* "csamtools.pyx":2597 * continue @@ -25046,7 +23771,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_pytype); __pyx_v_pytype = __pyx_t_13; __pyx_t_13 = 0; - goto __pyx_L14; + goto __pyx_L16; } /* "csamtools.pyx":2599 @@ -25094,7 +23819,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_pytype); __pyx_v_pytype = __pyx_t_7; __pyx_t_7 = 0; - goto __pyx_L16; + goto __pyx_L18; } /* "csamtools.pyx":2603 @@ -25119,7 +23844,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_pytype); __pyx_v_pytype = __pyx_t_13; __pyx_t_13 = 0; - goto __pyx_L16; + goto __pyx_L18; } /* "csamtools.pyx":2604 @@ -25137,7 +23862,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_13 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_13)); __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_7); + __Pyx_GOTREF(((PyObject *)__pyx_t_7)); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_13)); __Pyx_GIVEREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0; @@ -25147,7 +23872,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_Raise(__pyx_t_13, 0, 0, 0); __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L16; + goto __pyx_L18; } /*else*/ { @@ -25169,8 +23894,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_v_pytype = __pyx_t_7; __pyx_t_7 = 0; } - __pyx_L16:; - goto __pyx_L15; + __pyx_L18:; + goto __pyx_L17; } /*else*/ { @@ -25196,7 +23921,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_pytype); __pyx_v_pytype = __pyx_t_13; __pyx_t_13 = 0; - goto __pyx_L17; + goto __pyx_L19; } /* "csamtools.pyx":2609 @@ -25221,7 +23946,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_pytype); __pyx_v_pytype = __pyx_t_7; __pyx_t_7 = 0; - goto __pyx_L17; + goto __pyx_L19; } /* "csamtools.pyx":2610 @@ -25239,7 +23964,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_7)); __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_13); + __Pyx_GOTREF(((PyObject *)__pyx_t_13)); PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7)); __Pyx_GIVEREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; @@ -25249,7 +23974,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_Raise(__pyx_t_7, 0, 0, 0); __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L17; + goto __pyx_L19; } /*else*/ { @@ -25271,10 +23996,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_v_pytype = __pyx_t_13; __pyx_t_13 = 0; } - __pyx_L17:; + __pyx_L19:; } - __pyx_L15:; - goto __pyx_L14; + __pyx_L17:; + goto __pyx_L16; } /*else*/ { @@ -25303,9 +24028,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_DECREF(__pyx_v_value); __pyx_v_value = __pyx_t_7; __pyx_t_7 = 0; - goto __pyx_L18; + goto __pyx_L20; } - __pyx_L18:; + __pyx_L20:; /* "csamtools.pyx":2616 * if t is not bytes: @@ -25335,7 +24060,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_XDECREF(__pyx_v_pytype); __pyx_v_pytype = __pyx_t_13; __pyx_t_13 = 0; - goto __pyx_L19; + goto __pyx_L21; } /*else*/ { @@ -25361,9 +24086,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_v_pytype = __pyx_t_13; __pyx_t_13 = 0; } - __pyx_L19:; + __pyx_L21:; } - __pyx_L14:; + __pyx_L16:; /* "csamtools.pyx":2621 * fmt, pytype = "2sc%is" % (len(value)+1), 'Z' @@ -25398,7 +24123,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs * fmts.append( fmt ) */ __pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_14); @@ -25409,7 +24134,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __pyx_t_7 = 0; __pyx_t_14 = 0; __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_14); + __Pyx_GOTREF(((PyObject *)__pyx_t_14)); PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -25426,8 +24151,11 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs * * fmt = "".join(fmts) */ + if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_fmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(__pyx_v_fmt); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fmt); __Pyx_GIVEREF(__pyx_v_fmt); @@ -25551,19 +24279,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0; __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; - - /* "csamtools.pyx":2640 - * pysam_bam_update( src, - * src.l_aux, - * total_size, # <<<<<<<<<<<<<< - * bam1_aux( src ) ) - * - */ - if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; 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int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2691); __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.tid = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -25941,17 +24599,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csa return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); 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+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2730 * cdef bam1_t * src @@ -26384,7 +24972,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob * return None * return bam_calend(&src.core, */ - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -26410,9 +24998,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2732 * if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: @@ -26430,7 +25018,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob * * property mapq: */ - __pyx_t_2 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - __pyx_v_self->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -26450,17 +25038,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2738 * property mapq: * """mapping quality""" @@ -26469,7 +25046,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__py * */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) { int __pyx_r; __Pyx_RefNannyDeclarations uint32_t __pyx_t_1; @@ -26526,10 +25094,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2739); __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_qual); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.qual = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -26542,17 +25110,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9cs return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2745 * deprecated, use RNEXT instead. * """ @@ -26561,7 +25118,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__py * property rnext: */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) { int __pyx_r; __Pyx_RefNannyDeclarations int32_t __pyx_t_1; @@ -26618,10 +25166,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2746); __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2746; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.mtid = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -26634,17 +25182,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9cs return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2749 * property rnext: * """the :term:`reference` id of the mate """ @@ -26653,7 +25190,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__p * property mpos: */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -26661,10 +25199,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_o const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2749); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -26683,17 +25221,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_o return __pyx_r; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) { int __pyx_r; __Pyx_RefNannyDeclarations int32_t __pyx_t_1; @@ -26710,10 +25238,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9c const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2750); __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2750; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.mtid = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -26726,17 +25254,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9c return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2754 * """the position of the mate * deprecated, use PNEXT instead.""" @@ -26745,7 +25262,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__py * property pnext: */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) { int __pyx_r; __Pyx_RefNannyDeclarations int32_t __pyx_t_1; @@ -26802,10 +25310,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2755); __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.mpos = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -26818,17 +25326,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9cs return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2758 * property pnext: * """the position of the mate""" @@ -26837,7 +25334,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__p * property isize: */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) { int __pyx_r; __Pyx_RefNannyDeclarations int32_t __pyx_t_1; @@ -26894,10 +25382,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9c const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2759); __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2759; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.mpos = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -26910,17 +25398,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9c return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5isize___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2763 * """the insert size * deprecated: use tlen instead""" @@ -26929,7 +25406,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__p * property tlen: */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) { int __pyx_r; __Pyx_RefNannyDeclarations int32_t __pyx_t_1; @@ -26986,10 +25454,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9c const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2764); __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.isize = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -27002,17 +25470,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9c return __pyx_r; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) { int __pyx_r; __Pyx_RefNannyDeclarations int32_t __pyx_t_1; @@ -27078,10 +25526,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9cs const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2768); __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_self->_delegate->core.isize = __pyx_t_1; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1; __pyx_r = 0; goto __pyx_L0; @@ -27094,17 +25542,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9cs return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2771 * property is_paired: * """true if read is paired in sequencing""" @@ -27113,7 +25550,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject * if val: self._delegate.core.flag |= BAM_FPAIRED */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -27170,7 +25598,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2772); /* "csamtools.pyx":2773 @@ -27182,8 +25610,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 1); + goto __pyx_L5; } /*else*/ { @@ -27194,9 +25622,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob * property is_proper_pair: * """true if read is mapped in a proper pair""" */ - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1)); + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1)); } - __pyx_L3:; + __pyx_L5:; __pyx_r = 0; goto __pyx_L0; @@ -27209,17 +25637,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2777 * property is_proper_pair: * """true if read is mapped in a proper pair""" @@ -27228,7 +25645,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyO * if val: self._delegate.core.flag |= BAM_FPROPER_PAIR */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -27237,10 +25655,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(stru const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2777); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -27266,17 +25684,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(stru return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { - int __pyx_r; 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__Pyx_RefNannyDeclarations int __pyx_t_1; @@ -27293,7 +25701,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2778); /* "csamtools.pyx":2779 @@ -27305,8 +25713,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __ */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2779; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 2); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 2); + goto __pyx_L5; } /*else*/ { @@ -27317,9 +25725,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __ * property is_unmapped: * """true if read itself is unmapped""" */ - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~2)); + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~2)); } - __pyx_L3:; + __pyx_L5:; __pyx_r = 0; goto __pyx_L0; @@ -27332,17 +25740,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __ return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2783 * property is_unmapped: * """true if read itself is unmapped""" @@ -27351,7 +25748,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObje * if val: self._delegate.core.flag |= BAM_FUNMAP */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -27360,10 +25758,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2783); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -27389,17 +25787,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2784 * """true if read itself is unmapped""" * def __get__(self): return (self.flag & BAM_FUNMAP) != 0 @@ -27408,7 +25795,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__ * else: self._delegate.core.flag &= ~BAM_FUNMAP */ -static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) { +static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -27416,7 +25804,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2784); /* "csamtools.pyx":2785 @@ -27428,8 +25816,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 4); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 4); 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@@ -27539,7 +25907,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2790); /* "csamtools.pyx":2791 @@ -27551,8 +25919,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2791; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 8); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 8); + goto __pyx_L5; } /*else*/ { @@ -27563,9 +25931,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct * property is_reverse: * """true if read is mapped to reverse strand""" */ - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~8)); + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~8)); } - __pyx_L3:; + __pyx_L5:; __pyx_r = 0; goto __pyx_L0; @@ -27578,17 +25946,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2795 * property is_reverse: * """true if read is mapped to reverse strand""" @@ -27597,7 +25954,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObjec * if val: self._delegate.core.flag |= BAM_FREVERSE */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -27606,10 +25964,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct _ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2795); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -27635,17 +25993,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct _ return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2796 * """true if read is mapped to reverse strand""" * def __get__(self): return (self.flag & BAM_FREVERSE) != 0 @@ -27654,7 +26001,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__p * else: self._delegate.core.flag &= ~BAM_FREVERSE */ -static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) { +static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -27662,7 +26010,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2796); /* "csamtools.pyx":2797 @@ -27674,8 +26022,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_ */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2797; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 16); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 16); + goto __pyx_L5; } /*else*/ { @@ -27686,9 +26034,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_ * property mate_is_reverse: * """true is read is mapped to reverse strand""" */ - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~16)); + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~16)); } - __pyx_L3:; + __pyx_L5:; __pyx_r = 0; goto __pyx_L0; @@ -27701,17 +26049,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_ return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); 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int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2801); __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_32); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); @@ -27758,17 +26096,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(str return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/ -static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { - int __pyx_r; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__set__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2802 * """true is read is mapped to reverse strand""" * def __get__(self): return (self.flag & BAM_FMREVERSE) != 0 @@ -27777,7 +26104,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject * else: self._delegate.core.flag &= ~BAM_FMREVERSE */ -static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) { +static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -27785,7 +26113,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct _ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2802); /* "csamtools.pyx":2803 @@ -27797,8 +26125,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct _ */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 32); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 32); 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int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2808); /* "csamtools.pyx":2809 @@ -27920,8 +26228,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 64); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 64); + goto __pyx_L5; } /*else*/ { @@ -27932,9 +26240,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj * property is_read2: * """true if this is read2""" */ - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~64)); 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -28031,7 +26319,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2814); /* "csamtools.pyx":2815 @@ -28043,8 +26331,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2815; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 128); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 128); 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/*proto*/ +static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -28277,7 +26525,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__set__", 0); + __Pyx_RefNannySetupContext("__set__"); __Pyx_TraceCall("__set__", __pyx_f[0], 2826); /* "csamtools.pyx":2827 @@ -28289,8 +26537,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob */ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_1) { - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 512); - goto __pyx_L3; + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 512); + goto __pyx_L5; } /*else*/ { @@ -28301,9 +26549,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob * property is_duplicate: * """true if optical or PCR duplicate""" */ - __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~512)); + ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~512)); } - __pyx_L3:; + __pyx_L5:; __pyx_r = 0; goto __pyx_L0; @@ -28316,17 +26564,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); 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+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1024)); } - __pyx_L3:; + __pyx_L5:; __pyx_r = 0; goto __pyx_L0; @@ -28439,17 +26667,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __py return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9positions___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2837 * property positions: * """a list of reference positions that this read aligns to.""" @@ -28458,7 +26675,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject * cdef int op */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self) { uint32_t __pyx_v_k; uint32_t __pyx_v_i; uint32_t __pyx_v_pos; @@ -28479,7 +26697,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2837); /* "csamtools.pyx":2843 @@ -28489,7 +26707,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p * if src.core.n_cigar == 0: return [] * */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2844 * @@ -28502,13 +26720,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p if (__pyx_t_1) { __Pyx_XDECREF(__pyx_r); __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2846 * if src.core.n_cigar == 0: return [] @@ -28518,7 +26736,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p * cigar_p = bam1_cigar(src) */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_result = __pyx_t_2; __pyx_t_2 = 0; @@ -28605,14 +26823,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p * * if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_6 = PyList_Append(__pyx_v_result, __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } - goto __pyx_L6; + goto __pyx_L8; } - __pyx_L6:; + __pyx_L8:; /* "csamtools.pyx":2857 * result.append( i ) @@ -28673,17 +26894,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self); /*proto*/ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__get__ (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2867 * Unaligned position are marked by None. * """ @@ -28692,7 +26902,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyOb * cdef int op */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self) { uint32_t __pyx_v_k; uint32_t __pyx_v_i; uint32_t __pyx_v_pos; @@ -28715,7 +26926,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__get__", 0); + __Pyx_RefNannySetupContext("__get__"); __Pyx_TraceCall("__get__", __pyx_f[0], 2867); /* "csamtools.pyx":2873 @@ -28725,7 +26936,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc * if src.core.n_cigar == 0: return [] * */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2874 * @@ -28738,13 +26949,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc if (__pyx_t_1) { __Pyx_XDECREF(__pyx_r); __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_r = ((PyObject *)__pyx_t_2); __pyx_t_2 = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2876 * if src.core.n_cigar == 0: return [] @@ -28754,7 +26965,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc * qpos = 0 */ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2876; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __pyx_v_result = __pyx_t_2; __pyx_t_2 = 0; @@ -28858,12 +27069,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc * qpos += 1 * pos += l */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2); @@ -28932,10 +27146,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc * qpos += 1 * */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_6); __Pyx_INCREF(Py_None); @@ -28989,10 +27206,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc * pos += l * */ + if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) { + PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_INCREF(Py_None); PyTuple_SET_ITEM(__pyx_t_2, 0, Py_None); __Pyx_GIVEREF(Py_None); @@ -29051,29 +27271,58 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_9csamtools_11AlignedRead_10overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n "; -static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { +/* "csamtools.pyx":2904 + * + * + * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<< + * """return number of aligned bases of read overlapping the interval *start* and *end* + * on the reference sequence. + */ + +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ +static char __pyx_doc_9csamtools_11AlignedRead_5overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n "; +static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { uint32_t __pyx_v_start; uint32_t __pyx_v_end; - static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0}; - PyObject *__pyx_r = 0; + uint32_t __pyx_v_k; + uint32_t __pyx_v_pos; + uint32_t __pyx_v_overlap; + int __pyx_v_op; + int __pyx_v_o; + uint32_t *__pyx_v_cigar_p; + bam1_t *__pyx_v_src; + PyObject *__pyx_v_l = NULL; + PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("overlap (wrapper)", 0); + int __pyx_t_1; + uint32_t __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + uint32_t __pyx_t_4; + PyObject *__pyx_t_5 = NULL; + PyObject *__pyx_t_6 = NULL; + PyObject *__pyx_t_7 = NULL; + uint32_t __pyx_t_8; + uint32_t __pyx_t_9; + int __pyx_t_10; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0}; + __Pyx_TraceDeclarations + __Pyx_RefNannySetupContext("overlap"); + __Pyx_TraceCall("overlap", __pyx_f[0], 2904); { PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; - const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); - switch (pos_args) { + switch (PyTuple_GET_SIZE(__pyx_args)) { case 0: values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start); if (likely(values[0])) kw_args--; @@ -29086,7 +27335,7 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_s } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -29105,46 +27354,6 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_s __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10overlap(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), __pyx_v_start, __pyx_v_end); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - -/* "csamtools.pyx":2904 - * - * - * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<< - * """return number of aligned bases of read overlapping the interval *start* and *end* - * on the reference sequence. - */ - -static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end) { - uint32_t __pyx_v_k; - uint32_t __pyx_v_pos; - uint32_t __pyx_v_overlap; - int __pyx_v_op; - int __pyx_v_o; - uint32_t *__pyx_v_cigar_p; - bam1_t *__pyx_v_src; - PyObject *__pyx_v_l = NULL; - PyObject *__pyx_r = NULL; - __Pyx_RefNannyDeclarations - int __pyx_t_1; - uint32_t __pyx_t_2; - PyObject *__pyx_t_3 = NULL; - uint32_t __pyx_t_4; - PyObject *__pyx_t_5 = NULL; - PyObject *__pyx_t_6 = NULL; - PyObject *__pyx_t_7 = NULL; - uint32_t __pyx_t_8; - uint32_t __pyx_t_9; - int __pyx_t_10; - int __pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("overlap", 0); - __Pyx_TraceCall("overlap", __pyx_f[0], 2904); /* "csamtools.pyx":2913 * cdef bam1_t * src @@ -29162,7 +27371,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c * if src.core.n_cigar == 0: return 0 * pos = src.core.pos */ - __pyx_v_src = __pyx_v_self->_delegate; + __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate; /* "csamtools.pyx":2916 * @@ -29177,9 +27386,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c __Pyx_INCREF(__pyx_int_0); __pyx_r = __pyx_int_0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L6; } - __pyx_L3:; + __pyx_L6:; /* "csamtools.pyx":2917 * src = self._delegate @@ -29307,12 +27516,12 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c __pyx_t_1 = (__pyx_v_o > 0); if (__pyx_t_1) { __pyx_v_overlap = (__pyx_v_overlap + __pyx_v_o); - goto __pyx_L7; + goto __pyx_L10; } - __pyx_L7:; - goto __pyx_L6; + __pyx_L10:; + goto __pyx_L9; } - __pyx_L6:; + __pyx_L9:; /* "csamtools.pyx":2929 * if o > 0: overlap += o @@ -29376,18 +27585,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c return __pyx_r; } -/* Python wrapper */ -static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/ -static char __pyx_doc_9csamtools_11AlignedRead_12opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*"; -static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) { - PyObject *__pyx_r = 0; - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("opt (wrapper)", 0); - __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12opt(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tag)); - __Pyx_RefNannyFinishContext(); - return __pyx_r; -} - /* "csamtools.pyx":2934 * return overlap * @@ -29396,12 +27593,14 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, * #see bam_aux.c: bam_aux_get() and bam_aux2i() etc */ -static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag) { +static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/ +static char __pyx_doc_9csamtools_11AlignedRead_6opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*"; +static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) { uint8_t *__pyx_v_v; - CYTHON_UNUSED int __pyx_v_nvalues; + int __pyx_v_nvalues; PyObject *__pyx_v_btag = NULL; PyObject *__pyx_v_auxtype = NULL; - CYTHON_UNUSED PyObject *__pyx_v_bytesize = NULL; + PyObject *__pyx_v_bytesize = NULL; PyObject *__pyx_v_values = NULL; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations @@ -29422,7 +27621,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("opt", 0); + __Pyx_RefNannySetupContext("opt"); __Pyx_TraceCall("opt", __pyx_f[0], 2934); /* "csamtools.pyx":2939 @@ -29445,7 +27644,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt * auxtype = chr(v[0]) */ __pyx_t_2 = PyBytes_AsString(((PyObject *)__pyx_v_btag)); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2940; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_v = bam_aux_get(__pyx_v_self->_delegate, __pyx_t_2); + __pyx_v_v = bam_aux_get(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate, __pyx_t_2); /* "csamtools.pyx":2941 * btag = _force_bytes(tag) @@ -29459,7 +27658,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_148), __pyx_v_tag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __Pyx_GOTREF(((PyObject *)__pyx_t_4)); PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_1)); __Pyx_GIVEREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -29469,9 +27668,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; /* "csamtools.pyx":2942 * v = bam_aux_get(self._delegate, btag) @@ -29483,7 +27682,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((__pyx_v_v[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __Pyx_GOTREF(((PyObject *)__pyx_t_4)); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; @@ -29534,7 +27733,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - goto __pyx_L4; + goto __pyx_L6; } /* "csamtools.pyx":2945 @@ -29566,7 +27765,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - goto __pyx_L4; + goto __pyx_L6; } /* "csamtools.pyx":2947 @@ -29598,7 +27797,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - goto __pyx_L4; + goto __pyx_L6; } /* "csamtools.pyx":2949 @@ -29630,7 +27829,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - goto __pyx_L4; + goto __pyx_L6; } /* "csamtools.pyx":2951 @@ -29659,7 +27858,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_r = ((PyObject *)__pyx_t_4); __pyx_t_4 = 0; goto __pyx_L0; - goto __pyx_L4; + goto __pyx_L6; } /* "csamtools.pyx":2955 @@ -29685,7 +27884,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_r = __pyx_t_4; __pyx_t_4 = 0; goto __pyx_L0; - goto __pyx_L4; + goto __pyx_L6; } /* "csamtools.pyx":2957 @@ -29738,21 +27937,21 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __Pyx_GOTREF(__pyx_t_11); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext; - index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed; + index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_1); - index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L5_unpacking_failed; + index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_9); - index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L5_unpacking_failed; + index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L7_unpacking_failed; __Pyx_GOTREF(__pyx_t_10); if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; - goto __pyx_L6_unpacking_done; - __pyx_L5_unpacking_failed:; + goto __pyx_L8_unpacking_done; + __pyx_L7_unpacking_failed:; __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L6_unpacking_done:; + __pyx_L8_unpacking_done:; } __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; @@ -29773,7 +27972,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __Pyx_INCREF(__pyx_v_values); __pyx_r = __pyx_v_values; goto __pyx_L0; - goto __pyx_L4; + goto __pyx_L6; } /*else*/ { @@ -29787,7 +27986,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_149), __pyx_v_auxtype); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_4)); __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_10); + __Pyx_GOTREF(((PyObject *)__pyx_t_10)); PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_4)); __Pyx_GIVEREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; @@ -29798,7 +27997,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_L4:; 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/*proto*/ +static char __pyx_doc_9csamtools_11AlignedRead_7fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n "; +static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) { PyObject *__pyx_v_ret_string = NULL; PyObject *__pyx_v_field_names = NULL; PyObject *__pyx_v_fields_names_in_order = NULL; @@ -29863,7 +28052,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_ const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("fancy_str", 0); + __Pyx_RefNannySetupContext("fancy_str"); __Pyx_TraceCall("fancy_str", __pyx_f[0], 2964); /* "csamtools.pyx":2967 @@ -29874,7 +28063,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_ * "tid": "Contig index", */ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2967; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __pyx_v_ret_string = __pyx_t_1; __pyx_t_1 = 0; @@ -29916,7 +28105,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_ * "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"] */ __pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(((PyObject *)__pyx_n_s__tid)); PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tid)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__tid)); @@ -29981,6 +28170,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_ * if not f in self.__dict__: * continue */ + if (unlikely(((PyObject *)__pyx_v_fields_names_in_order) == Py_None)) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_t_1 = __pyx_f_9csamtools_makePileupRead((&((((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -30712,20 +28846,6 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx return __pyx_r; } -/* Python wrapper */ -static int __pyx_pw_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static int __pyx_pw_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { - int __pyx_r; 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__pyx_lineno = 0; - const char *__pyx_filename = NULL; - int __pyx_clineno = 0; - __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("_samtools_dispatch", 0); - __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3125); __Pyx_INCREF(__pyx_v_method); __Pyx_INCREF(__pyx_v_args); __Pyx_INCREF(__pyx_v_catch_stdout); @@ -32297,7 +30276,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); + __Pyx_GOTREF(((PyObject *)__pyx_t_4)); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = 0; @@ -32323,7 +30302,7 @@ static PyObject 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*__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext; - index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed; + index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_3); - index = 1; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L5_unpacking_failed; + index = 1; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - goto __pyx_L6_unpacking_done; - __pyx_L5_unpacking_failed:; + goto __pyx_L9_unpacking_done; + __pyx_L8_unpacking_failed:; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L6_unpacking_done:; + __pyx_L9_unpacking_done:; } __pyx_v_stderr_h = __pyx_t_3; __pyx_t_3 = 0; @@ -32465,19 +30444,19 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext; - index = 0; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed; + index = 0; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L11_unpacking_failed; __Pyx_GOTREF(__pyx_t_2); - index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed; + index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L11_unpacking_failed; __Pyx_GOTREF(__pyx_t_3); if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - goto __pyx_L9_unpacking_done; - __pyx_L8_unpacking_failed:; + goto __pyx_L12_unpacking_done; + __pyx_L11_unpacking_failed:; __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear(); if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_L9_unpacking_done:; + __pyx_L12_unpacking_done:; } __pyx_v_stdout_h = __pyx_t_2; __pyx_t_2 = 0; @@ -32505,25 +30484,25 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * * stdout_save.setfd( stdout_h ) * except AttributeError: */ - __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; @@ -32537,14 +30516,14 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * * except AttributeError: * # stdout has already been redirected */ - __pyx_t_2 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;} - __Pyx_GOTREF(__pyx_t_3); + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); __Pyx_INCREF(__pyx_v_stdout_h); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_h); __Pyx_GIVEREF(__pyx_v_stdout_h); - __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;} + __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; @@ -32553,8 +30532,8 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0; __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0; - goto __pyx_L17_try_end; - __pyx_L10_error:; + goto __pyx_L20_try_end; + __pyx_L13_error:; __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -32570,7 +30549,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_AttributeError); if (__pyx_t_8) { __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;} + if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GOTREF(__pyx_t_3); __Pyx_GOTREF(__pyx_t_2); @@ -32582,7 +30561,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * * * # patch for `samtools view` */ - __pyx_t_6 = 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__pyx_L14_exception_handled:; __Pyx_XGIVEREF(__pyx_t_9); __Pyx_XGIVEREF(__pyx_t_10); __Pyx_XGIVEREF(__pyx_t_11); __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11); - __pyx_L17_try_end:; + __pyx_L20_try_end:; } /* "csamtools.pyx":3171 @@ -32630,9 +30609,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L21; + goto __pyx_L24; } - __pyx_L21:; + __pyx_L24:; /* "csamtools.pyx":3173 * if method == "view": @@ -32642,7 +30621,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * * # do the function call to samtools */ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_178)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_178)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_178)); @@ -32655,12 +30634,12 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_DECREF(__pyx_v_args); __pyx_v_args = __pyx_t_3; __pyx_t_3 = 0; - goto __pyx_L20; + goto __pyx_L23; } - __pyx_L20:; - goto __pyx_L7; + __pyx_L23:; + goto __pyx_L10; } - __pyx_L7:; + __pyx_L10:; /* "csamtools.pyx":3179 * cdef int i, n, retval @@ -32693,7 +30672,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * * # allocate two more for first (dummy) argument (contains command) */ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); + __Pyx_GOTREF(((PyObject *)__pyx_t_3)); if (PyList_CheckExact(__pyx_v_args) || PyTuple_CheckExact(__pyx_v_args)) { __pyx_t_2 = __pyx_v_args; __Pyx_INCREF(__pyx_t_2); __pyx_t_12 = 0; __pyx_t_13 = NULL; @@ -32703,10 +30682,10 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __pyx_t_13 = Py_TYPE(__pyx_t_2)->tp_iternext; } for (;;) { - if (!__pyx_t_13 && PyList_CheckExact(__pyx_t_2)) { + if (PyList_CheckExact(__pyx_t_2)) { if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_2)) break; __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++; - } else if (!__pyx_t_13 && PyTuple_CheckExact(__pyx_t_2)) { + } else if (PyTuple_CheckExact(__pyx_t_2)) { if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_2)) break; __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++; } else { @@ -32805,6 +30784,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * */ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3194; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__pyx_t_5) { + if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_3 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":3195 * # needs to be before reading back the file contents @@ -32813,8 +30793,6 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * * try: * with open( stdout_f, "r") as inf: */ - if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_t_3 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; 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}__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); __Pyx_INCREF(__pyx_v_stdout_f); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f); __Pyx_GIVEREF(__pyx_v_stdout_f); __Pyx_INCREF(((PyObject *)__pyx_n_s__r)); PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__r)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r)); - __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;} + __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; - __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;} + __Pyx_GOTREF(__pyx_t_2); __Pyx_GOTREF(__pyx_t_3); __Pyx_GOTREF(__pyx_t_4); - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __Pyx_INCREF(__pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_2); + __Pyx_GIVEREF(__pyx_t_2); __Pyx_INCREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_4); - PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); - 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__Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0; + __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0; __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0; - __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0; + __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; - __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; /* "csamtools.pyx":3210 * pysam_unset_stderr() @@ -33305,74 +31278,74 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * */ /*except:*/ { __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;} - __Pyx_GOTREF(__pyx_t_3); + if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_2, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_GOTREF(__pyx_t_2); - __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;} - __Pyx_GOTREF(__pyx_t_6); - __Pyx_INCREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3); - __Pyx_GIVEREF(__pyx_t_3); + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_21 = PyTuple_New(3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_21)); __Pyx_INCREF(__pyx_t_4); - PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __Pyx_INCREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_2); + PyTuple_SET_ITEM(__pyx_t_21, 1, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); - __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL); + __Pyx_INCREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_21, 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__pyx_t_4 = 0; __pyx_t_2 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;} + __Pyx_GIVEREF(__pyx_t_3); + __Pyx_ErrRestore(__pyx_t_4, __pyx_t_2, __pyx_t_3); + __pyx_t_4 = 0; __pyx_t_2 = 0; __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;} goto __pyx_L100; } __pyx_L100:; - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - goto __pyx_L90_exception_handled; + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + goto __pyx_L91_exception_handled; } - __pyx_L91_except_error:; + __pyx_L92_except_error:; __Pyx_XGIVEREF(__pyx_t_16); __Pyx_XGIVEREF(__pyx_t_17); __Pyx_XGIVEREF(__pyx_t_18); __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18); - goto __pyx_L75_error; - __pyx_L90_exception_handled:; + goto __pyx_L76_error; + __pyx_L91_exception_handled:; __Pyx_XGIVEREF(__pyx_t_16); __Pyx_XGIVEREF(__pyx_t_17); __Pyx_XGIVEREF(__pyx_t_18); __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18); - __pyx_L96_try_end:; + __pyx_L97_try_end:; } } /*finally:*/ { if (__pyx_t_15) { __pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_183, NULL); __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0; - if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;} + if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;} __Pyx_GOTREF(__pyx_t_18); __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18); __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0; - if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;} + if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 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__pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;} + if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_2, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;} + __Pyx_GOTREF(__pyx_t_3); __Pyx_GOTREF(__pyx_t_2); __Pyx_GOTREF(__pyx_t_4); - __Pyx_GOTREF(__pyx_t_3); /* "csamtools.pyx":3213 * out_stderr = inf.readlines() @@ -33427,24 +31400,24 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * * out_stderr = inf.read() */ /*with:*/ { - __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_21 = PyTuple_New(2); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_21)); __Pyx_INCREF(__pyx_v_stderr_f); - PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f); + PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_v_stderr_f); __Pyx_GIVEREF(__pyx_v_stderr_f); __Pyx_INCREF(((PyObject *)__pyx_n_s__rb)); - PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb)); + PyTuple_SET_ITEM(__pyx_t_21, 1, ((PyObject *)__pyx_n_s__rb)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb)); - __pyx_t_21 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;} - __Pyx_GOTREF(__pyx_t_21); - __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __pyx_t_15 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;} + __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_21), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;} + __Pyx_GOTREF(__pyx_t_20); + __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0; + __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;} __Pyx_GOTREF(__pyx_t_15); - __pyx_t_6 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;} - __Pyx_GOTREF(__pyx_t_6); - __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;} + __pyx_t_21 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;} + __Pyx_GOTREF(__pyx_t_21); + __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; + __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;} __Pyx_GOTREF(__pyx_t_20); - __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; /*try:*/ { { @@ -33453,10 +31426,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_XGOTREF(__pyx_t_17); __Pyx_XGOTREF(__pyx_t_16); /*try:*/ { - __Pyx_INCREF(__pyx_t_20); __Pyx_XDECREF(__pyx_v_inf); __pyx_v_inf = __pyx_t_20; - __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; + __pyx_t_20 = 0; /* "csamtools.pyx":3215 * with open( stderr_f, "rb") as inf: @@ -33498,7 +31470,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_GOTREF(__pyx_t_20); __Pyx_GOTREF(__pyx_t_6); __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;} - __Pyx_GOTREF(__pyx_t_22); + __Pyx_GOTREF(((PyObject *)__pyx_t_22)); __Pyx_INCREF(__pyx_t_21); PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_21); __Pyx_GIVEREF(__pyx_t_21); @@ -33523,9 +31495,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_ErrRestore(__pyx_t_21, __pyx_t_20, __pyx_t_6); __pyx_t_21 = 0; __pyx_t_20 = 0; __pyx_t_6 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;} - goto __pyx_L121; + goto __pyx_L120; } - __pyx_L121:; + __pyx_L120:; __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0; __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0; __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0; @@ -33537,7 +31509,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject * __Pyx_XGIVEREF(__pyx_t_17); __Pyx_XGIVEREF(__pyx_t_16); __Pyx_ExceptionReset(__pyx_t_18, 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__pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); /* "csamtools.pyx":3271 @@ -34140,7 +32020,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool * self.genotype, * self.consensus_quality, */ - __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); /* "csamtools.pyx":3272 @@ -34150,7 +32030,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool * self.consensus_quality, * self.snp_quality, */ - __pyx_t_5 = PyObject_GetAttr(((PyObject 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(__pyx_t_1) { /* "csamtools.pyx":3829 @@ -34754,13 +32595,13 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam * raise KeyError( "read %s not found" % qname ) */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile)); - PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self->samfile)); - __Pyx_GIVEREF(((PyObject 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; __pyx_r = __pyx_t_4; __pyx_t_4 = 0; goto __pyx_L0; - goto __pyx_L3; + goto __pyx_L5; } /*else*/ { @@ -34791,7 +32632,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_186), __pyx_v_qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_4)); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4)); __Pyx_GIVEREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; @@ -34802,7 +32643,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - __pyx_L3:; + __pyx_L5:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -34819,15 +32660,6 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam return __pyx_r; } -/* Python wrapper */ -static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self); /*proto*/ -static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self) { - __Pyx_RefNannyDeclarations - __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); - __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)); - __Pyx_RefNannyFinishContext(); -} - /* "csamtools.pyx":3833 * raise KeyError( "read %s not found" % qname ) * @@ -34836,10 +32668,11 @@ static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_se * */ -static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self) { +static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self); /*proto*/ +static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_TraceDeclarations - __Pyx_RefNannySetupContext("__dealloc__", 0); + __Pyx_RefNannySetupContext("__dealloc__"); __Pyx_TraceCall("__dealloc__", __pyx_f[0], 3833); /* "csamtools.pyx":3834 @@ -34849,11 +32682,11 @@ static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9cs * * __all__ = ["Samfile", */ - if (__pyx_v_self->owns_samfile) { - samclose(__pyx_v_self->fp); - goto __pyx_L3; + if (((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile) { + samclose(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp); + goto __pyx_L5; } - __pyx_L3:; + __pyx_L5:; __Pyx_TraceReturn(Py_None); __Pyx_RefNannyFinishContext(); @@ -34866,7 +32699,7 @@ static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, if (!o) return 0; p = ((struct __pyx_obj_9csamtools_Fastafile *)o); p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile; - if (__pyx_pw_9csamtools_9Fastafile_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -34877,7 +32710,7 @@ static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_9Fastafile_11__dealloc__(o); + __pyx_pf_9csamtools_9Fastafile_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -34886,14 +32719,14 @@ static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) { } static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) { - return __pyx_pw_9csamtools_9Fastafile_8filename_1__get__(o); + return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o); } static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = { - {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_2_isOpen)}, - {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_7_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6_open)}, - {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_9close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_8close)}, - {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_13fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_12fetch)}, + {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_1_isOpen)}, + {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)}, + {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_4close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_4close)}, + {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_6fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6fetch)}, {0, 0, 0, 0} }; @@ -34961,7 +32794,7 @@ static PyNumberMethods __pyx_tp_as_number_Fastafile = { }; static PySequenceMethods __pyx_tp_as_sequence_Fastafile = { - __pyx_pw_9csamtools_9Fastafile_5__len__, /*sq_length*/ + __pyx_pf_9csamtools_9Fastafile_2__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ @@ -34974,7 +32807,7 @@ static PySequenceMethods __pyx_tp_as_sequence_Fastafile = { }; static PyMappingMethods __pyx_tp_as_mapping_Fastafile = { - __pyx_pw_9csamtools_9Fastafile_5__len__, /*mp_length*/ + __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; @@ -35067,7 +32900,7 @@ static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(o); + __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -35076,12 +32909,12 @@ static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) { } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5qname___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35090,12 +32923,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35104,12 +32937,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35118,12 +32951,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObj } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_3seq___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35132,12 +32965,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4qual___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35146,32 +32979,32 @@ static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5query_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5query___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4qend___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4tags___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35180,12 +33013,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35194,12 +33027,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35208,12 +33041,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35222,12 +33055,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35236,12 +33069,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35250,24 +33083,24 @@ static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35276,12 +33109,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35290,12 +33123,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35304,12 +33137,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35318,12 +33151,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35332,12 +33165,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35346,12 +33179,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35360,12 +33193,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35374,12 +33207,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObjec } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35388,12 +33221,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, Py } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35402,12 +33235,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObj } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35416,12 +33249,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35430,12 +33263,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObje } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35444,12 +33277,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, P } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35458,12 +33291,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35472,12 +33305,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35486,12 +33319,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyOb } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35500,12 +33333,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObjec } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o); } static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v); + return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -35514,18 +33347,18 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyOb } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o); } static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o); + return __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(o); } static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = { - {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_7compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6compare)}, - {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_11overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_10overlap)}, - {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_13opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_12opt)}, - {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_15fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_14fancy_str)}, + {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_3compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_3compare)}, + {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_5overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_5overlap)}, + {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_6opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6opt)}, + {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_7fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_7fancy_str)}, {0, 0, 0, 0} }; @@ -35688,9 +33521,9 @@ static PyTypeObject __pyx_type_9csamtools_AlignedRead = { &__pyx_tp_as_number_AlignedRead, /*tp_as_number*/ &__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/ &__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/ - __pyx_pw_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/ + __pyx_pf_9csamtools_11AlignedRead_4__hash__, /*tp_hash*/ 0, /*tp_call*/ - __pyx_pw_9csamtools_11AlignedRead_5__str__, /*tp_str*/ + __pyx_pf_9csamtools_11AlignedRead_2__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/ @@ -35710,7 +33543,7 @@ static PyTypeObject __pyx_type_9csamtools_AlignedRead = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_9csamtools_11AlignedRead_1__init__, /*tp_init*/ + __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/ 0, /*tp_free*/ @@ -35733,7 +33566,7 @@ static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, P if (!o) return 0; p = ((struct __pyx_obj_9csamtools_Samfile *)o); p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile; - if (__pyx_pw_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -35744,7 +33577,7 @@ static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_7Samfile_31__dealloc__(o); + __pyx_pf_9csamtools_7Samfile_15__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -35753,57 +33586,57 @@ static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) { } static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_8filename_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_8filename___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_10references_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_10references___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_7lengths_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_6mapped_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_4text_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_4text___get__(o); } static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7Samfile_6header_1__get__(o); + return __pyx_pf_9csamtools_7Samfile_6header___get__(o); } static PyMethodDef __pyx_methods_9csamtools_Samfile[] = { - {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_isOpen)}, - {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4_hasIndex)}, - {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_open)}, - {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8gettid)}, - {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10getrname)}, - {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12_parseRegion)}, - {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14reset)}, - {__Pyx_NAMESTR("seek"), 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__Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_28close)}, - {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_32write)}, - {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_34__enter__)}, - {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_36__exit__)}, - {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_38_buildLine)}, - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_42__next__)}, + {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)}, + {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)}, + {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)}, + {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)}, + {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)}, + {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)}, + {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)}, + {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)}, + {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)}, + {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)}, + {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)}, + {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)}, + {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)}, + {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)}, + {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)}, + {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)}, + {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)}, + {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)}, {0, 0, 0, 0} }; @@ -35947,8 +33780,8 @@ static PyTypeObject __pyx_type_9csamtools_Samfile = { 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_9csamtools_7Samfile_41__iter__, /*tp_iter*/ - __pyx_pw_9csamtools_7Samfile_43__next__, /*tp_iternext*/ + __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/ + __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/ __pyx_methods_9csamtools_Samfile, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_9csamtools_Samfile, /*tp_getset*/ @@ -35984,16 +33817,16 @@ static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) { } static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(o); + return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o); } static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11PileupProxy_1n_1__get__(o); + return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o); } static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) { if (v) { - return __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(o, v); + return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); @@ -36002,11 +33835,11 @@ static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, vo } static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(o); + return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o); } static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) { - return __pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(o); + return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o); } static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = { @@ -36139,7 +33972,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = { &__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - __pyx_pw_9csamtools_11PileupProxy_3__str__, /*tp_str*/ + __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/ @@ -36159,7 +33992,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_9csamtools_11PileupProxy_1__init__, /*tp_init*/ + __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/ 0, /*tp_free*/ @@ -36209,31 +34042,31 @@ static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) { } static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) { - return __pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(o); + return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o); } static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) { - return __pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(o); + return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o); } static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) { - return __pyx_pw_9csamtools_10PileupRead_5indel_1__get__(o); + return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o); } static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) { - return __pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(o); + return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o); } static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) { - return __pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(o); + return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o); } static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) { - return __pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(o); + return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o); } static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) { - return __pyx_pw_9csamtools_10PileupRead_5level_1__get__(o); + return __pyx_pf_9csamtools_10PileupRead_5level___get__(o); } static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = { @@ -36369,7 +34202,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupRead = { &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - __pyx_pw_9csamtools_10PileupRead_3__str__, /*tp_str*/ + __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/ @@ -36389,7 +34222,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupRead = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_9csamtools_10PileupRead_1__init__, /*tp_init*/ + __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/ 0, /*tp_free*/ @@ -36581,7 +34414,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyOb p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o); p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion; p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); - if (__pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -36593,7 +34426,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(o); + __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -36627,7 +34460,7 @@ static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) { } static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_4__next__)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)}, {0, 0, 0, 0} }; @@ -36759,8 +34592,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = { __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/ - __pyx_pw_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/ + __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/ + __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ @@ -36792,7 +34625,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObjec if (!o) return 0; p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o); p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll; - if (__pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -36803,7 +34636,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(o); + __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -36812,7 +34645,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) { } static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_4__next__)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)}, {0, 0, 0, 0} }; @@ -36944,8 +34777,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = { 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/ - __pyx_pw_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/ + __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/ + __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ @@ -36977,7 +34810,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyO 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_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -37021,8 +34854,8 @@ static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) { } static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = { - {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_2nextiter)}, - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__)}, + {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)}, {0, 0, 0, 0} }; @@ -37154,8 +34987,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = { __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/ - __pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/ + __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/ + __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ @@ -37188,7 +35021,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, P p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o); p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection; p->positions = Py_None; Py_INCREF(Py_None); - if (__pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -37200,7 +35033,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(o); + __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -37234,7 +35067,7 @@ static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) { } static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_4__next__)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)}, {0, 0, 0, 0} }; @@ -37366,8 +35199,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = { __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/ - __pyx_pw_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/ + __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/ + __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ @@ -37403,7 +35236,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObjec p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None); p->stepper = Py_None; Py_INCREF(Py_None); - if (__pyx_pw_9csamtools_14IteratorColumn_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; @@ -37415,7 +35248,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(o); + __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -37464,12 +35297,12 @@ static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) { } static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) { - return __pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(o); + return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o); } static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = { - {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_4addReference)}, - {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pw_9csamtools_14IteratorColumn_7hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_6hasReference)}, + {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)}, + {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)}, {0, 0, 0, 0} }; @@ -37606,7 +35439,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = { __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/ + __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/ 0, /*tp_members*/ @@ -37639,14 +35472,14 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, P if (!o) return 0; p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion; - if (__pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_2__next__)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)}, {0, 0, 0, 0} }; @@ -37779,7 +35612,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = { 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ - __pyx_pw_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/ + __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ @@ -37811,14 +35644,14 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, if (!o) return 0; p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs; - if (__pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) { + if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = { - {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__)}, + {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)}, {0, 0, 0, 0} }; @@ -37951,7 +35784,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = { 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ - __pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/ + __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/ __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ @@ -37992,7 +35825,7 @@ static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); - __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(o); + __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); @@ -38027,8 +35860,8 @@ static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) { } static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = { - {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pw_9csamtools_12IndexedReads_3build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2build)}, - {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_4find)}, + {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_1build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_1build)}, + {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)}, {0, 0, 0, 0} }; @@ -38170,7 +36003,7 @@ static PyTypeObject __pyx_type_9csamtools_IndexedReads = { 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ - __pyx_pw_9csamtools_12IndexedReads_1__init__, /*tp_init*/ + __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_9csamtools_IndexedReads, /*tp_new*/ 0, /*tp_free*/ @@ -38197,35 +36030,35 @@ static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) { } static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_3tid_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o); } static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_3pos_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o); } static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o); } static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o); } static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o); } static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o); } static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o); } static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) { - return __pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(o); + return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o); } static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = { @@ -38362,7 +36195,7 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = { &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ - __pyx_pw_9csamtools_7SNPCall_1__str__, /*tp_str*/ + __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/ @@ -38398,9 +36231,219 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = { #endif }; +static PyObject *__pyx_tp_new_9csamtools___pyx_Generator(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_Generator_object *p; + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + p = ((struct __pyx_Generator_object *)o); + p->exc_type = 0; + p->exc_value = 0; + p->exc_traceback = 0; + return o; +} + +static void __pyx_tp_dealloc_9csamtools___pyx_Generator(PyObject *o) { + struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o; + Py_XDECREF(p->exc_type); + Py_XDECREF(p->exc_value); + Py_XDECREF(p->exc_traceback); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_9csamtools___pyx_Generator(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o; + if (p->exc_type) { + e = (*v)(p->exc_type, a); if (e) return e; + } + if (p->exc_value) { + e = (*v)(p->exc_value, a); if (e) return e; + } + if (p->exc_traceback) { + e = (*v)(p->exc_traceback, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_9csamtools___pyx_Generator(PyObject *o) { + struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o; + PyObject* tmp; + tmp = ((PyObject*)p->exc_type); + p->exc_type = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->exc_value); + p->exc_value = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->exc_traceback); + p->exc_traceback = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_9csamtools___pyx_Generator[] = { + {__Pyx_NAMESTR("send"), (PyCFunction)__Pyx_Generator_Send, METH_O, __Pyx_DOCSTR(0)}, + {__Pyx_NAMESTR("close"), (PyCFunction)__Pyx_Generator_Close, METH_NOARGS, __Pyx_DOCSTR(0)}, + {__Pyx_NAMESTR("throw"), (PyCFunction)__Pyx_Generator_Throw, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, + {0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number___pyx_Generator = { + 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___pyx_Generator = { + 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___pyx_Generator = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer___pyx_Generator = { + #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 +}; + +static PyTypeObject __pyx_Generator_type = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("csamtools.__pyx_Generator"), /*tp_name*/ + sizeof(struct __pyx_Generator_object), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_9csamtools___pyx_Generator, /*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___pyx_Generator, /*tp_as_number*/ + &__pyx_tp_as_sequence___pyx_Generator, /*tp_as_sequence*/ + &__pyx_tp_as_mapping___pyx_Generator, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer___pyx_Generator, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_9csamtools___pyx_Generator, /*tp_traverse*/ + __pyx_tp_clear_9csamtools___pyx_Generator, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + PyObject_SelfIter, /*tp_iter*/ + __Pyx_Generator_Next, /*tp_iternext*/ + __pyx_methods_9csamtools___pyx_Generator, /*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___pyx_Generator, /*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___pyx_scope_struct__genexpr(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p; - PyObject *o = (*t->tp_alloc)(t, 0); + PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o); p->__pyx_v_x = 0; @@ -38416,12 +36459,13 @@ static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr(PyObject *o) Py_XDECREF(p->__pyx_v_y); Py_XDECREF(p->__pyx_t_0); Py_XDECREF(p->__pyx_t_1); - (*Py_TYPE(o)->tp_free)(o); + __pyx_tp_dealloc_9csamtools___pyx_Generator(o); } static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o; + e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e; if (p->__pyx_v_x) { e = (*v)(p->__pyx_v_x, a); if (e) return e; } @@ -38440,6 +36484,7 @@ static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o, static int __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr(PyObject *o) { struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o; PyObject* tmp; + __pyx_tp_clear_9csamtools___pyx_Generator(o); tmp = ((PyObject*)p->__pyx_v_x); p->__pyx_v_x = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); @@ -38615,7 +36660,7 @@ static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = { static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p; - PyObject *o = (*t->tp_alloc)(t, 0); + PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o); p->__pyx_v_x = 0; @@ -38631,12 +36676,13 @@ static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o Py_XDECREF(p->__pyx_v_y); Py_XDECREF(p->__pyx_t_0); Py_XDECREF(p->__pyx_t_1); - (*Py_TYPE(o)->tp_free)(o); + __pyx_tp_dealloc_9csamtools___pyx_Generator(o); } static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o; + e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e; if (p->__pyx_v_x) { e = (*v)(p->__pyx_v_x, a); if (e) return e; } @@ -38655,6 +36701,7 @@ static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o static int __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) { struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o; PyObject* tmp; + __pyx_tp_clear_9csamtools___pyx_Generator(o); tmp = ((PyObject*)p->__pyx_v_x); p->__pyx_v_x = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); @@ -38913,12 +36960,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0}, {&__pyx_n_s_249, __pyx_k_249, sizeof(__pyx_k_249), 0, 0, 1, 1}, {&__pyx_kp_s_251, __pyx_k_251, sizeof(__pyx_k_251), 0, 0, 1, 0}, + {&__pyx_kp_s_254, __pyx_k_254, sizeof(__pyx_k_254), 0, 0, 1, 0}, + {&__pyx_kp_s_255, __pyx_k_255, 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__pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_4); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_4)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii)); PyTuple_SET_ITEM(__pyx_k_tuple_4, 0, ((PyObject *)__pyx_n_s__ascii)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); @@ -39294,7 +37329,7 @@ static int __Pyx_InitCachedConstants(void) { * return faidx_fetch_nseq(self.fastafile) */ __pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_8); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_8)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_7)); PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_kp_s_7)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7)); @@ -39308,7 +37343,7 @@ static int __Pyx_InitCachedConstants(void) { * */ __pyx_k_tuple_11 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_11); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_11)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_11, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -39322,7 +37357,7 @@ static int __Pyx_InitCachedConstants(void) { * cdef int length */ __pyx_k_tuple_12 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_12); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_12)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_12, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -39336,7 +37371,7 @@ static int __Pyx_InitCachedConstants(void) { * if end is None: end = max_pos -1 */ __pyx_k_tuple_14 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; 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__pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_25); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_25)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii)); PyTuple_SET_ITEM(__pyx_k_tuple_25, 0, ((PyObject *)__pyx_n_s__ascii)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); @@ -39378,7 +37413,7 @@ static int __Pyx_InitCachedConstants(void) { * return pysam_reference2tid( self.samfile.header, reference ) */ __pyx_k_tuple_39 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_39); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_39)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_39, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -39392,7 +37427,7 @@ static int __Pyx_InitCachedConstants(void) { * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) */ 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static int __Pyx_InitCachedConstants(void) { * rtid = self.gettid( reference ) */ __pyx_k_tuple_44 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_44); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_44)); __Pyx_INCREF(__pyx_int_0); PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, __pyx_int_0); __Pyx_GIVEREF(__pyx_int_0); @@ -39443,7 +37478,7 @@ static int __Pyx_InitCachedConstants(void) { * raise NotImplementedError("seek only available in bam files") */ __pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_47); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_47)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -39457,7 +37492,7 @@ 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_74); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_74)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_74, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -39653,7 +37688,7 @@ static int __Pyx_InitCachedConstants(void) { * if not region: */ __pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_75); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_75)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_56)); PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_kp_s_56)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56)); @@ -39667,7 +37702,7 @@ static int __Pyx_InitCachedConstants(void) { * bam_fetch(self.samfile.x.bam, */ __pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_77); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_77)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_76)); PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_kp_s_76)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76)); @@ -39681,7 +37716,7 @@ static int __Pyx_InitCachedConstants(void) { * self.index, */ __pyx_k_tuple_78 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_78); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_78)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_60)); PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_kp_s_60)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60)); @@ -39695,7 +37730,7 @@ static int __Pyx_InitCachedConstants(void) { * def pileup( self, */ __pyx_k_tuple_80 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_80)) 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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); @@ -39978,7 +38013,7 @@ static int __Pyx_InitCachedConstants(void) { * dest.target_len[x] = seqlen */ __pyx_k_tuple_114 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_114)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_114); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_114)); __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii)); PyTuple_SET_ITEM(__pyx_k_tuple_114, 0, ((PyObject *)__pyx_n_s__ascii)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii)); @@ -39992,7 +38027,7 @@ static int __Pyx_InitCachedConstants(void) { * raise NotImplementedError( "can not iterate over samfile without header") */ __pyx_k_tuple_115 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_115)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_115); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_115)); __Pyx_INCREF(((PyObject 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__Pyx_GOTREF(((PyObject *)__pyx_k_tuple_121)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_121, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -40062,7 +38097,7 @@ static int __Pyx_InitCachedConstants(void) { * self.tid = -1 */ __pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_122); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_122)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_60)); PyTuple_SET_ITEM(__pyx_k_tuple_122, 0, ((PyObject *)__pyx_kp_s_60)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60)); @@ -40076,7 +38111,7 @@ static int __Pyx_InitCachedConstants(void) { * if not samfile._isOpen(): */ __pyx_k_tuple_123 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_123)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_123); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_123)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_123, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -40090,7 +38125,7 @@ static int __Pyx_InitCachedConstants(void) { * assert samfile.isbam, "can only use this iterator on bam files" */ __pyx_k_tuple_124 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_124); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_124)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_10)); PyTuple_SET_ITEM(__pyx_k_tuple_124, 0, ((PyObject *)__pyx_kp_s_10)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10)); @@ -40104,7 +38139,7 @@ static int __Pyx_InitCachedConstants(void) { * if self.plp == NULL: */ __pyx_k_tuple_130 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_130)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_130); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_130)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_129)); PyTuple_SET_ITEM(__pyx_k_tuple_130, 0, ((PyObject *)__pyx_kp_s_129)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129)); @@ -40118,7 +38153,7 @@ static int __Pyx_InitCachedConstants(void) { * # return result, if within same reference */ __pyx_k_tuple_131 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_k_tuple_131); + __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_131)); __Pyx_INCREF(((PyObject *)__pyx_kp_s_129)); PyTuple_SET_ITEM(__pyx_k_tuple_131, 0, ((PyObject *)__pyx_kp_s_129)); __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129)); @@ -40132,7 +38167,7 @@ static int __Pyx_InitCachedConstants(void) { * return "\t".join(map(str, (self.qname, */ __pyx_k_tuple_133 = PyTuple_New(1); if 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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 /*--- Library function declarations ---*/ /*--- Threads initialization code ---*/ @@ -40910,9 +38663,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__.doc = __pyx_doc_9csamtools_11AlignedRead_4__str__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_4__str__; + __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__.doc = __pyx_doc_9csamtools_11AlignedRead_2__str__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_2__str__; } } if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -40927,9 +38680,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_9csamtools_7Samfile_42__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_9csamtools_7Samfile_42__next__.doc = __pyx_doc_9csamtools_7Samfile_42__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_42__next__; + __pyx_wrapperbase_9csamtools_7Samfile_21__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_7Samfile_21__next__.doc = __pyx_doc_9csamtools_7Samfile_21__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_21__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -40952,9 +38705,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_4__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__; + __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_2__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -40968,9 +38721,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_4__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__; + __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_2__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -40981,9 +38734,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__; + __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__; } } if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -40996,9 +38749,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_4__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__; + __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_2__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41021,9 +38774,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { - __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; - __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_2__next__; - ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__; + __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__; } } if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41036,9 +38789,9 @@ PyMODINIT_FUNC PyInit_csamtools(void) { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41050,8 +38803,12 @@ PyMODINIT_FUNC PyInit_csamtools(void) if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __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 = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall; + if (PyType_Ready(&__pyx_Generator_type) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_9csamtools___pyx_Generator = &__pyx_Generator_type; + __pyx_type_9csamtools___pyx_scope_struct__genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator; if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_9csamtools___pyx_scope_struct__genexpr; + __pyx_type_9csamtools___pyx_scope_struct_1_genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator; if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_9csamtools___pyx_scope_struct_1_genexpr; /*--- Type import code ---*/ @@ -41317,10 +39074,10 @@ PyMODINIT_FUNC PyInit_csamtools(void) * else: * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) */ - __pyx_t_1 = __pyx_pf_9csamtools_2genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_pf_9csamtools_1genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; @@ -41340,10 +39097,10 @@ PyMODINIT_FUNC PyInit_csamtools(void) * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) * */ - __pyx_t_1 = __pyx_pf_9csamtools_5genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_pf_9csamtools_3genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __Pyx_GOTREF(((PyObject *)__pyx_t_2)); PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; @@ -41417,7 +39174,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ * "\n" + "\n".join( map(str, self.pileups) ) */ - __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_12PileupColumn_1__str__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_255)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_12PileupColumn___str__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____str__, 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__pyx_L1_error;} __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; @@ -41459,7 +39216,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * return * self.stderr_h, self.stderr_f = tempfile.mkstemp() */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_259)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41471,7 +39228,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * return [] * self.stderr_save.restore() */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_3readAndRelease, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_261)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41483,7 +39240,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * return * self.stderr_save.restore() */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_5release, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_263)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41495,7 +39252,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * self.release() * */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_7__del__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_265)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_3__del__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____del__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41507,7 +39264,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * ''' * stderr is captured. */ - if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_266)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_255)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41531,7 +39288,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * def readAndRelease(self): return [] * def release(self): pass */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_268)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41543,7 +39300,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * def release(self): pass * */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_3readAndRelease, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_270)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41555,7 +39312,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * * if platform.system()=='Windows': */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_5release, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_272)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41567,7 +39324,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * '''does nothing. stderr can't be redirected on windows''' * def __init__(self): pass */ - if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_273)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_256)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStoreWindows, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41673,7 +39430,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * * # type conversions within sam header records */ - if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_274)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_257)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":357 * @@ -41697,7 +39454,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, # <<<<<<<<<<<<<< * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, - * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str }, + * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, */ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_4)); @@ -41714,8 +39471,8 @@ PyMODINIT_FUNC PyInit_csamtools(void) * VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, # <<<<<<<<<<<<<< - * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str }, - * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, } + * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, + * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } */ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_4)); @@ -41729,8 +39486,8 @@ PyMODINIT_FUNC PyInit_csamtools(void) /* "csamtools.pyx":360 * "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, - * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str }, # <<<<<<<<<<<<<< - * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, } + * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, # <<<<<<<<<<<<<< + * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } * */ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41738,13 +39495,14 @@ PyMODINIT_FUNC PyInit_csamtools(void) if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__FO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__KS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; /* "csamtools.pyx":361 * "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, - * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str }, - * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, } # <<<<<<<<<<<<<< + * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, + * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } # <<<<<<<<<<<<<< * * # output order of fields within records */ @@ -41754,6 +39512,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41764,38 +39523,38 @@ PyMODINIT_FUNC PyInit_csamtools(void) * # output order of fields within records * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<< * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), - * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), + * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), */ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_275)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_258)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":365 * # output order of fields within records * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<< - * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), - * "PG" : ( "PN", "ID", "VN", "CL" ), } + * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), + * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } */ - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_276)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_259)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":366 * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), - * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), # <<<<<<<<<<<<<< - * "PG" : ( "PN", "ID", "VN", "CL" ), } + * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), # <<<<<<<<<<<<<< + * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } * */ - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_277)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_260)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "csamtools.pyx":367 * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), - * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), - * "PG" : ( "PN", "ID", "VN", "CL" ), } # <<<<<<<<<<<<<< + * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), + * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<< * * */ - if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_278)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_261)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; @@ -41890,9 +39649,8 @@ PyMODINIT_FUNC PyInit_csamtools(void) * self.streams = [] * self.id = id */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_280)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_4, ((PyObject *)__pyx_k_tuple_281)); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41903,7 +39661,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * '''open an existing file, like "/dev/null"''' * fd = os.open(filename, os.O_WRONLY) */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_3setdevice, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_283)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_1setdevice, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setdevice, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41915,7 +39673,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * '''open a new file.''' * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660); */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_5setfile, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_285)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_2setfile, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfile, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41927,7 +39685,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * ofd = os.dup(self.id) # Save old stream on new unit. * self.streams.append(ofd) */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_7setfd, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_287)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_3setfd, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfd, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41939,7 +39697,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * '''restore previous output stream''' * if self.streams: */ - __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_9restore, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_289)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_4restore, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__restore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -41951,7 +39709,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html''' * def __init__(self, id = 1): */ - if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_290)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_262)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__Outs, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -41978,7 +39736,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * args = (), * catch_stdout = True ): */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9csamtools_1_samtools_dispatch, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9csamtools__samtools_dispatch, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -41991,7 +39749,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) * "IteratorRow", */ __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); + __Pyx_GOTREF(((PyObject *)__pyx_t_1)); __Pyx_INCREF(((PyObject *)__pyx_n_s__Samfile)); PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Samfile)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__Samfile)); @@ -42052,6 +39810,7 @@ PyMODINIT_FUNC PyInit_csamtools(void) } /* Runtime support code */ + #if CYTHON_REFNANNY static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { PyObject *m = NULL, *p = NULL; @@ -42083,7 +39842,9 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) { return result; } + #if CYTHON_PROFILE + static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, @@ -42107,10 +39868,12 @@ static int __Pyx_TraceSetupAndCall(PyCodeObject** code, } return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0; } + static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) { PyObject *py_srcfile = 0; PyObject *py_funcname = 0; PyCodeObject *py_code = 0; + #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); py_srcfile = PyString_FromString(srcfile); @@ -42119,6 +39882,7 @@ static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const cha py_srcfile = PyUnicode_FromString(srcfile); #endif if (!py_funcname | !py_srcfile) goto bad; + py_code = PyCode_New( 0, /*int argcount,*/ #if PY_MAJOR_VERSION >= 3 @@ -42138,17 +39902,20 @@ static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const cha firstlineno, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); + bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); + return py_code; } + #endif /* CYTHON_PROFILE */ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { -#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; @@ -42158,30 +39925,27 @@ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyOb Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); -#else - PyErr_Restore(type, value, tb); -#endif } + static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { -#if CYTHON_COMPILING_IN_CPYTHON 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; -#else - PyErr_Fetch(type, value, tb); -#endif } + #if PY_MAJOR_VERSION < 3 -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, - CYTHON_UNUSED PyObject *cause) { +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + /* cause is unused */ 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; @@ -42191,6 +39955,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, "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); @@ -42201,11 +39966,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, 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 , */ Py_DECREF(value); value = type; #if PY_VERSION_HEX < 0x02050000 @@ -42229,6 +39996,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, } #endif } + __Pyx_ErrRestore(type, value, tb); return; raise_error: @@ -42237,7 +40005,9 @@ raise_error: Py_XDECREF(tb); return; } + #else /* Python 3+ */ + static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { if (tb == Py_None) { tb = 0; @@ -42248,6 +40018,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } if (value == Py_None) value = 0; + if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, @@ -42261,6 +40032,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject "raise: exception class must be a subclass of BaseException"); goto bad; } + if (cause) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { @@ -42283,7 +40055,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } PyException_SetCause(value, fixed_cause); } + PyErr_SetObject(type, value); + if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; @@ -42293,6 +40067,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject Py_XDECREF(tmp_tb); } } + bad: return; } @@ -42321,7 +40096,7 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings( #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) #else - if (unlikely(!PyUnicode_Check(key))) + if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) #endif goto invalid_keyword_type; } @@ -42369,6 +40144,7 @@ static int __Pyx_ParseOptionalKeywords( 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++; @@ -42378,7 +40154,7 @@ static int __Pyx_ParseOptionalKeywords( #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) { #else - if (unlikely(!PyUnicode_Check(key))) { + if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) { #endif goto invalid_keyword_type; } else { @@ -42394,6 +40170,7 @@ static int __Pyx_ParseOptionalKeywords( 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 @@ -42443,6 +40220,7 @@ static void __Pyx_RaiseArgtupleInvalid( { Py_ssize_t num_expected; const char *more_or_less; + if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; @@ -42575,7 +40353,6 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { } - static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; @@ -42585,6 +40362,7 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, 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(); @@ -42625,33 +40403,12 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { goto bad; #if PY_VERSION_HEX >= 0x02050000 { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { - /* try package relative import first */ - PyObject *py_level = PyInt_FromLong(1); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; /* try absolute import on failure */ - } - #endif - if (!module) { - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - } + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); } #else if (level>0) { @@ -42698,8 +40455,10 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na PyObject *modname) { PyObject *result; PyObject *metaclass; + if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; + /* Python2 __metaclass__ */ metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { @@ -42712,367 +40471,48 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na return result; } -static PyObject * -__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) -{ - if (op->func_doc == NULL && op->func.m_ml->ml_doc) { -#if PY_MAJOR_VERSION >= 3 - op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); -#else - op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); -#endif - } - if (op->func_doc == 0) { - Py_INCREF(Py_None); - return Py_None; - } - Py_INCREF(op->func_doc); - return op->func_doc; -} -static int -__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) -{ - PyObject *tmp = op->func_doc; - if (value == NULL) - op->func_doc = Py_None; /* Mark as deleted */ - else - op->func_doc = value; - Py_INCREF(op->func_doc); - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) -{ - if (op->func_name == NULL) { -#if PY_MAJOR_VERSION >= 3 - op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); -#else - op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); -#endif - } - Py_INCREF(op->func_name); - return op->func_name; -} -static int -__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) -{ - PyObject *tmp; -#if PY_MAJOR_VERSION >= 3 - if (value == NULL || !PyUnicode_Check(value)) { -#else - if (value == NULL || !PyString_Check(value)) { -#endif - PyErr_SetString(PyExc_TypeError, - "__name__ must be set to a string object"); - return -1; - } - tmp = op->func_name; - Py_INCREF(value); - op->func_name = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) -{ - PyObject *self; - self = m->func_closure; - if (self == NULL) - self = Py_None; - Py_INCREF(self); - return self; -} -static PyObject * -__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) -{ - if (op->func_dict == NULL) { - op->func_dict = PyDict_New(); - if (op->func_dict == NULL) - return NULL; - } - Py_INCREF(op->func_dict); - return op->func_dict; -} -static int -__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) -{ - PyObject *tmp; - if (value == NULL) { - PyErr_SetString(PyExc_TypeError, - "function's dictionary may not be deleted"); - return -1; - } - if (!PyDict_Check(value)) { - PyErr_SetString(PyExc_TypeError, - "setting function's dictionary to a non-dict"); - return -1; - } - tmp = op->func_dict; - Py_INCREF(value); - op->func_dict = value; - Py_XDECREF(tmp); - return 0; -} -static PyObject * -__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op) -{ - PyObject* dict = PyModule_GetDict(__pyx_m); - Py_XINCREF(dict); - return dict; -} -static PyObject * -__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) -{ - Py_INCREF(Py_None); - return Py_None; -} -static PyObject * -__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) -{ - PyObject* result = (op->func_code) ? op->func_code : Py_None; - Py_INCREF(result); - return result; -} -static PyObject * -__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) -{ - if (op->defaults_tuple) { - Py_INCREF(op->defaults_tuple); - return op->defaults_tuple; - } - if (op->defaults_getter) { - PyObject *res = op->defaults_getter((PyObject *) op); - if (res) { - Py_INCREF(res); - op->defaults_tuple = res; - } - return res; - } - Py_INCREF(Py_None); - return Py_None; -} -static PyGetSetDef __pyx_CyFunction_getsets[] = { - {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, - {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, - {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, - {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, - {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, - {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, - {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, - {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, - {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, - {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, - {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, - {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, - {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, - {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, - {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, - {0, 0, 0, 0, 0} -}; -#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */ -#define PY_WRITE_RESTRICTED WRITE_RESTRICTED -#endif -static PyMemberDef __pyx_CyFunction_members[] = { - {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, - {0, 0, 0, 0, 0} -}; -static PyObject * -__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) -{ -#if PY_MAJOR_VERSION >= 3 - return PyUnicode_FromString(m->func.m_ml->ml_name); -#else - return PyString_FromString(m->func.m_ml->ml_name); -#endif -} -static PyMethodDef __pyx_CyFunction_methods[] = { - {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, - {0, 0, 0, 0} -}; -static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, - PyObject *closure, PyObject *module, PyObject* code) { - __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); + +static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) { + __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType); if (op == NULL) return NULL; - op->flags = flags; - op->func_weakreflist = NULL; op->func.m_ml = ml; - op->func.m_self = (PyObject *) op; - Py_XINCREF(closure); - op->func_closure = closure; + Py_XINCREF(self); + op->func.m_self = self; Py_XINCREF(module); op->func.m_module = module; - op->func_dict = NULL; - op->func_name = NULL; - op->func_doc = NULL; - op->func_classobj = NULL; - Py_XINCREF(code); - op->func_code = code; - op->defaults_pyobjects = 0; - op->defaults = NULL; - op->defaults_tuple = NULL; - op->defaults_getter = NULL; PyObject_GC_Track(op); - return (PyObject *) op; -} -static int -__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) -{ - Py_CLEAR(m->func_closure); - Py_CLEAR(m->func.m_module); - Py_CLEAR(m->func_dict); - Py_CLEAR(m->func_name); - Py_CLEAR(m->func_doc); - Py_CLEAR(m->func_code); - Py_CLEAR(m->func_classobj); - Py_CLEAR(m->defaults_tuple); - if (m->defaults) { - PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); - int i; - for (i = 0; i < m->defaults_pyobjects; i++) - Py_XDECREF(pydefaults[i]); - PyMem_Free(m->defaults); - m->defaults = NULL; - } - return 0; + return (PyObject *)op; } -static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) -{ + +static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) { PyObject_GC_UnTrack(m); - if (m->func_weakreflist != NULL) - PyObject_ClearWeakRefs((PyObject *) m); - __Pyx_CyFunction_clear(m); + Py_XDECREF(m->func.m_self); + Py_XDECREF(m->func.m_module); PyObject_GC_Del(m); } -static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) -{ - Py_VISIT(m->func_closure); - Py_VISIT(m->func.m_module); - Py_VISIT(m->func_dict); - Py_VISIT(m->func_name); - Py_VISIT(m->func_doc); - Py_VISIT(m->func_code); - Py_VISIT(m->func_classobj); - Py_VISIT(m->defaults_tuple); - if (m->defaults) { - PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); - int i; - for (i = 0; i < m->defaults_pyobjects; i++) - Py_VISIT(pydefaults[i]); - } - return 0; -} -static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) -{ - __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; - if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { - Py_INCREF(func); - return func; - } - if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { - if (type == NULL) - type = (PyObject *)(Py_TYPE(obj)); - return PyMethod_New(func, - type, (PyObject *)(Py_TYPE(type))); - } + +static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) { if (obj == Py_None) - obj = NULL; + obj = NULL; return PyMethod_New(func, obj, type); } -static PyObject* -__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) -{ - PyObject *func_name = __Pyx_CyFunction_get_name(op); -#if PY_MAJOR_VERSION >= 3 - return PyUnicode_FromFormat("", - func_name, (void *)op); -#else - return PyString_FromFormat("", - PyString_AsString(func_name), (void *)op); -#endif -} -static PyTypeObject __pyx_CyFunctionType_type = { - PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ - sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/ - 0, /*tp_print*/ - 0, /*tp_getattr*/ - 0, /*tp_setattr*/ -#if PY_MAJOR_VERSION < 3 - 0, /*tp_compare*/ -#else - 0, /*reserved*/ -#endif - (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/ - 0, /*tp_as_number*/ - 0, /*tp_as_sequence*/ - 0, /*tp_as_mapping*/ - 0, /*tp_hash*/ - __Pyx_PyCFunction_Call, /*tp_call*/ - 0, /*tp_str*/ - 0, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ - 0, /*tp_doc*/ - (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/ - (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/ - 0, /*tp_richcompare*/ - offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */ - 0, /*tp_iter*/ - 0, /*tp_iternext*/ - __pyx_CyFunction_methods, /*tp_methods*/ - __pyx_CyFunction_members, /*tp_members*/ - __pyx_CyFunction_getsets, /*tp_getset*/ - 0, /*tp_base*/ - 0, /*tp_dict*/ - __Pyx_CyFunction_descr_get, /*tp_descr_get*/ - 0, /*tp_descr_set*/ - offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/ - 0, /*tp_init*/ - 0, /*tp_alloc*/ - 0, /*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 int __Pyx_CyFunction_init(void) -{ - if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) + +static int __pyx_binding_PyCFunctionType_init(void) { + __pyx_binding_PyCFunctionType_type = PyCFunction_Type; + __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method"); + __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc; + __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get; + if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) { return -1; - __pyx_CyFunctionType = &__pyx_CyFunctionType_type; + } + __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type; return 0; -} -void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) -{ - __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; - m->defaults = PyMem_Malloc(size); - if (!m->defaults) - return PyErr_NoMemory(); - memset(m->defaults, 0, sizeof(size)); - m->defaults_pyobjects = pyobjects; - return m->defaults; -} -static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) -{ - __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; - m->defaults_tuple = tuple; - Py_INCREF(tuple); + } static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { - if (s1 == s2) { + if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */ return (equals == Py_EQ); } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) { @@ -43102,26 +40542,16 @@ static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int eq } static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { - if (s1 == s2) { + if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */ return (equals == Py_EQ); } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { - #if CYTHON_PEP393_ENABLED - if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0)) - return -1; - if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) { - return (equals == Py_NE); - } else if (PyUnicode_GET_LENGTH(s1) == 1) { - Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0); - Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0); - return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); - #else if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { return (equals == Py_NE); } else if (PyUnicode_GET_SIZE(s1) == 1) { - Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0]; - Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0]; - return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); - #endif + if (equals == Py_EQ) + return (PyUnicode_AS_UNICODE(s1)[0] == PyUnicode_AS_UNICODE(s2)[0]); + else + return (PyUnicode_AS_UNICODE(s1)[0] != PyUnicode_AS_UNICODE(s2)[0]); } else { int result = PyUnicode_Compare(s1, s2); if ((result == -1) && unlikely(PyErr_Occurred())) @@ -43954,79 +41384,86 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; 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; + *type = tmp_type; *value = tmp_value; *tb = tmp_tb; } -static PyObject *__Pyx_Generator_Next(PyObject *self); -static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); -static PyObject *__Pyx_Generator_Close(PyObject *self); -static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args); -static CYTHON_INLINE -void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) +static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self) { - PyObject *exc_type = self->exc_type; - PyObject *exc_value = self->exc_value; - PyObject *exc_traceback = self->exc_traceback; + Py_XDECREF(self->exc_type); + Py_XDECREF(self->exc_value); + Py_XDECREF(self->exc_traceback); + self->exc_type = NULL; self->exc_value = NULL; self->exc_traceback = NULL; - Py_XDECREF(exc_type); - Py_XDECREF(exc_value); - Py_XDECREF(exc_traceback); } -static CYTHON_INLINE -PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) + +static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value) { PyObject *retval; - if (unlikely(self->is_running)) { + + if (self->is_running) { PyErr_SetString(PyExc_ValueError, "generator already executing"); return NULL; } - if (unlikely(self->resume_label == 0)) { - if (unlikely(value && value != Py_None)) { + + if (self->resume_label == 0) { + if (value && value != Py_None) { PyErr_SetString(PyExc_TypeError, "can't send non-None value to a " "just-started generator"); return NULL; } } - if (unlikely(self->resume_label == -1)) { + + if (self->resume_label == -1) { PyErr_SetNone(PyExc_StopIteration); return NULL; } + + if (value) __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); else __Pyx_Generator_ExceptionClear(self); + self->is_running = 1; retval = self->body((PyObject *) self, value); self->is_running = 0; + if (retval) __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); else __Pyx_Generator_ExceptionClear(self); + return retval; } + static PyObject *__Pyx_Generator_Next(PyObject *self) { - return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None); + return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None); } + static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) { - return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value); + return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value); } + static PyObject *__Pyx_Generator_Close(PyObject *self) { - __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; + struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self; PyObject *retval; #if PY_VERSION_HEX < 0x02050000 PyErr_SetNone(PyExc_StopIteration); @@ -44053,190 +41490,19 @@ static PyObject *__Pyx_Generator_Close(PyObject *self) } return NULL; } -static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) + +static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds) { - __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self; + struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self; PyObject *typ; PyObject *tb = NULL; PyObject *val = NULL; + if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) return NULL; __Pyx_Raise(typ, val, tb, NULL); return __Pyx_Generator_SendEx(generator, NULL); } -static int -__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) -{ - __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; - Py_VISIT(gen->closure); - Py_VISIT(gen->classobj); - Py_VISIT(gen->exc_type); - Py_VISIT(gen->exc_value); - Py_VISIT(gen->exc_traceback); - return 0; -} -static void -__Pyx_Generator_dealloc(PyObject *self) -{ - __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; - PyObject_GC_UnTrack(gen); - if (gen->gi_weakreflist != NULL) - PyObject_ClearWeakRefs(self); - PyObject_GC_Track(self); - if (gen->resume_label > 0) { - Py_TYPE(gen)->tp_del(self); - if (self->ob_refcnt > 0) - return; /* resurrected. :( */ - } - PyObject_GC_UnTrack(self); - Py_CLEAR(gen->closure); - Py_CLEAR(gen->classobj); - Py_CLEAR(gen->exc_type); - Py_CLEAR(gen->exc_value); - Py_CLEAR(gen->exc_traceback); - PyObject_GC_Del(gen); -} -static void -__Pyx_Generator_del(PyObject *self) -{ - PyObject *res; - PyObject *error_type, *error_value, *error_traceback; - __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; - if (gen->resume_label <= 0) - return ; - assert(self->ob_refcnt == 0); - self->ob_refcnt = 1; - __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); - res = __Pyx_Generator_Close(self); - if (res == NULL) - PyErr_WriteUnraisable(self); - else - Py_DECREF(res); - __Pyx_ErrRestore(error_type, error_value, error_traceback); - /* Undo the temporary resurrection; can't use DECREF here, it would - * cause a recursive call. - */ - assert(self->ob_refcnt > 0); - if (--self->ob_refcnt == 0) - return; /* this is the normal path out */ - /* close() resurrected it! Make it look like the original Py_DECREF - * never happened. - */ - { - Py_ssize_t refcnt = self->ob_refcnt; - _Py_NewReference(self); - self->ob_refcnt = refcnt; - } - assert(PyType_IS_GC(self->ob_type) && - _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); - /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so - * we need to undo that. */ - _Py_DEC_REFTOTAL; - /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object - * chain, so no more to do there. - * If COUNT_ALLOCS, the original decref bumped tp_frees, and - * _Py_NewReference bumped tp_allocs: both of those need to be - * undone. - */ -#ifdef COUNT_ALLOCS - --self->ob_type->tp_frees; - --self->ob_type->tp_allocs; -#endif -} -static PyMemberDef __pyx_Generator_memberlist[] = { - {(char *) "gi_running", - T_INT, - offsetof(__pyx_GeneratorObject, is_running), - READONLY, - NULL}, - {0, 0, 0, 0, 0} -}; -static PyMethodDef __pyx_Generator_methods[] = { - {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0}, - {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0}, - {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0}, - {0, 0, 0, 0} -}; -static PyTypeObject __pyx_GeneratorType = { - PyVarObject_HEAD_INIT(0, 0) - __Pyx_NAMESTR("generator"), /*tp_name*/ - sizeof(__pyx_GeneratorObject), /*tp_basicsize*/ - 0, /*tp_itemsize*/ - (destructor) __Pyx_Generator_dealloc,/*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*/ - 0, /*tp_as_number*/ - 0, /*tp_as_sequence*/ - 0, /*tp_as_mapping*/ - 0, /*tp_hash*/ - 0, /*tp_call*/ - 0, /*tp_str*/ - PyObject_GenericGetAttr, /*tp_getattro*/ - 0, /*tp_setattro*/ - 0, /*tp_as_buffer*/ - Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ - 0, /*tp_doc*/ - (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/ - 0, /*tp_clear*/ - 0, /*tp_richcompare*/ - offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */ - PyObject_SelfIter, /*tp_iter*/ - (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/ - __pyx_Generator_methods, /*tp_methods*/ - __pyx_Generator_memberlist, /*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*/ - 0, /*tp_new*/ - 0, /*tp_free*/ - 0, /*tp_is_gc*/ - 0, /*tp_bases*/ - 0, /*tp_mro*/ - 0, /*tp_cache*/ - 0, /*tp_subclasses*/ - 0, /*tp_weaklist*/ - __Pyx_Generator_del, /*tp_del*/ -#if PY_VERSION_HEX >= 0x02060000 - 0, /*tp_version_tag*/ -#endif -}; -static -__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, - PyObject *closure) -{ - __pyx_GeneratorObject *gen = - PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType); - if (gen == NULL) - return NULL; - gen->body = body; - gen->closure = closure; - Py_XINCREF(closure); - gen->is_running = 0; - gen->resume_label = 0; - gen->classobj = NULL; - gen->exc_type = NULL; - gen->exc_value = NULL; - gen->exc_traceback = NULL; - gen->gi_weakreflist = NULL; - PyObject_GC_Track(gen); - return gen; -} -static int __pyx_Generator_init(void) -{ - return PyType_Ready(&__pyx_GeneratorType); -} static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename) { @@ -44302,10 +41568,15 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class PyObject *result = 0; PyObject *py_name = 0; char warning[200]; + py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; - py_name = __Pyx_PyIdentifier_FromString(class_name); + #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); @@ -44321,7 +41592,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class module_name, class_name); goto bad; } - if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) { + if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); @@ -44331,7 +41602,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } - else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) { + else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); @@ -44350,7 +41621,12 @@ bad: static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; - py_name = __Pyx_PyIdentifier_FromString(name); + + #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); @@ -44362,105 +41638,29 @@ bad: } #endif -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = (start + end) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - #include "compile.h" #include "frameobject.h" #include "traceback.h" -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; + +static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno, + int __pyx_lineno, const char *__pyx_filename) { 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(filename); + py_srcfile = PyString_FromString(__pyx_filename); #else - py_srcfile = PyUnicode_FromString(filename); + py_srcfile = PyUnicode_FromString(__pyx_filename); #endif if (!py_srcfile) goto bad; - if (c_line) { + if (__pyx_clineno) { #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno); #endif } else { @@ -44471,45 +41671,28 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( #endif } if (!py_funcname) goto bad; - py_code = __Pyx_PyCode_New( + 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,*/ + __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,*/ - py_line, /*int firstlineno,*/ + __pyx_lineno, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); - Py_DECREF(py_srcfile); - Py_DECREF(py_funcname); - return py_code; -bad: - Py_XDECREF(py_srcfile); - Py_XDECREF(py_funcname); - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyObject *py_globals = 0; - PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); - if (!py_code) { - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) goto bad; - __pyx_insert_code_object(c_line ? c_line : py_line, py_code); - } - py_globals = PyModule_GetDict(__pyx_m); - if (!py_globals) goto bad; + if (!py_code) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ @@ -44517,9 +41700,11 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; - py_frame->f_lineno = py_line; + 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); } @@ -44554,7 +41739,6 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { return 0; } - /* Type Conversion Functions */ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { diff --git a/pysam/csamtools.pyx b/pysam/csamtools.pyx index 7dd075c..e300c66 100644 --- a/pysam/csamtools.pyx +++ b/pysam/csamtools.pyx @@ -357,14 +357,14 @@ VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, - "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str }, - "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, } + "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, + "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } # output order of fields within records VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), - "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), - "PG" : ( "PN", "ID", "VN", "CL" ), } + "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), + "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } ###################################################################### diff --git a/pysam/ctabix.c b/pysam/ctabix.c index 9ab49e7..005213c 100644 --- a/pysam/ctabix.c +++ b/pysam/ctabix.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.17.1 on Tue Nov 20 16:47:00 2012 */ +/* Generated by Cython 0.17.4 on Mon Jan 14 21:45:57 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -53,12 +53,15 @@ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) - #define PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && !PyComplex_Check(o)) + #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ + !PyComplex_Check(o)) + #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" + #define __Pyx_PyIndex_Check PyIndex_Check #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) @@ -355,21 +358,21 @@ static const char *__pyx_f[] = { /*--- Type declarations ---*/ struct __pyx_obj_6ctabix_Parser; -struct __pyx_obj_6ctabix_asVCF; +struct __pyx_obj_6ctabix_asGTF; +struct __pyx_obj_6ctabix_Tabixfile; struct __pyx_obj_10TabProxies_TupleProxy; struct __pyx_obj_10TabProxies_NamedTupleProxy; -struct __pyx_obj_10TabProxies_BedProxy; -struct __pyx_obj_6ctabix_tabix_copy_iterator; struct __pyx_obj_10TabProxies_VCFProxy; -struct __pyx_obj_10TabProxies_GTFProxy; -struct __pyx_obj_6ctabix_TabixIterator; +struct __pyx_obj_6ctabix_tabix_inplace_iterator; +struct __pyx_obj_6ctabix_tabix_copy_iterator; struct __pyx_obj_6ctabix_TabixIteratorParsed; +struct __pyx_obj_10TabProxies_BedProxy; struct __pyx_obj_6ctabix_TabixHeaderIterator; -struct __pyx_obj_6ctabix_Tabixfile; -struct __pyx_obj_6ctabix_asGTF; -struct __pyx_obj_6ctabix_asBed; -struct __pyx_obj_6ctabix_tabix_inplace_iterator; struct __pyx_obj_6ctabix_asTuple; +struct __pyx_obj_10TabProxies_GTFProxy; +struct __pyx_obj_6ctabix_asBed; +struct __pyx_obj_6ctabix_TabixIterator; +struct __pyx_obj_6ctabix_asVCF; /* "ctabix.pxd":190 * cdef tabix_t * tabixfile @@ -383,18 +386,33 @@ struct __pyx_obj_6ctabix_Parser { }; -/* "ctabix.pxd":202 +/* "ctabix.pxd":196 * pass * - * cdef class asVCF(Parser): # <<<<<<<<<<<<<< + * cdef class asGTF(Parser): # <<<<<<<<<<<<<< * pass * */ -struct __pyx_obj_6ctabix_asVCF { +struct __pyx_obj_6ctabix_asGTF { struct __pyx_obj_6ctabix_Parser __pyx_base; }; +/* "ctabix.pxd":172 + * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) + * + * cdef class Tabixfile: # <<<<<<<<<<<<<< + * + * # pointer to tabixfile + */ +struct __pyx_obj_6ctabix_Tabixfile { + PyObject_HEAD + tabix_t *tabixfile; + int isremote; + char *_filename; +}; + + /* "TabProxies.pxd":41 * ctypedef int uint64_t * @@ -427,37 +445,6 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy { }; -/* "TabProxies.pxd":72 - * 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; -}; - - -/* "ctabix.pxd":218 - * cdef __cnext__(self) - * - * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef Parser parser - */ -struct __pyx_obj_6ctabix_tabix_copy_iterator { - PyObject_HEAD - struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab; - FILE *infile; - struct __pyx_obj_6ctabix_Parser *parser; -}; - - /* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * @@ -472,31 +459,35 @@ struct __pyx_obj_10TabProxies_VCFProxy { }; -/* "TabProxies.pxd":60 - * cdef update( self, char * buffer, size_t nbytes ) - * - * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< +/* "ctabix.pxd":210 + * cdef Parser parser * - * cdef: + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef char * buffer */ -struct __pyx_obj_10TabProxies_GTFProxy { - struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; - char *_attributes; - int hasOwnAttributes; +struct __pyx_obj_6ctabix_tabix_inplace_iterator { + PyObject_HEAD + struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab; + FILE *infile; + char *buffer; + size_t size; + struct __pyx_obj_6ctabix_Parser *parser; }; -/* "ctabix.pxd":182 - * cdef char * _filename +/* "ctabix.pxd":218 + * cdef __cnext__(self) * - * cdef class TabixIterator: # <<<<<<<<<<<<<< - * cdef ti_iter_t iterator - * cdef tabix_t * tabixfile + * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< + * cdef FILE * infile + * cdef Parser parser */ -struct __pyx_obj_6ctabix_TabixIterator { +struct __pyx_obj_6ctabix_tabix_copy_iterator { PyObject_HEAD - ti_iter_t iterator; - tabix_t *tabixfile; + struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab; + FILE *infile; + struct __pyx_obj_6ctabix_Parser *parser; }; @@ -515,6 +506,22 @@ struct __pyx_obj_6ctabix_TabixIteratorParsed { }; +/* "TabProxies.pxd":72 + * 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; +}; + + /* "ctabix.pxd":186 * cdef tabix_t * tabixfile * @@ -529,30 +536,29 @@ struct __pyx_obj_6ctabix_TabixHeaderIterator { }; -/* "ctabix.pxd":172 - * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) +/* "ctabix.pxd":193 + * pass * - * cdef class Tabixfile: # <<<<<<<<<<<<<< + * cdef class asTuple(Parser): # <<<<<<<<<<<<<< + * pass * - * # pointer to tabixfile */ -struct __pyx_obj_6ctabix_Tabixfile { - PyObject_HEAD - tabix_t *tabixfile; - int isremote; - char *_filename; +struct __pyx_obj_6ctabix_asTuple { + struct __pyx_obj_6ctabix_Parser __pyx_base; }; -/* "ctabix.pxd":196 - * pass +/* "TabProxies.pxd":60 + * cdef update( self, char * buffer, size_t nbytes ) * - * cdef class asGTF(Parser): # <<<<<<<<<<<<<< - * pass + * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * + * cdef: */ -struct __pyx_obj_6ctabix_asGTF { - struct __pyx_obj_6ctabix_Parser __pyx_base; +struct __pyx_obj_10TabProxies_GTFProxy { + struct __pyx_obj_10TabProxies_TupleProxy __pyx_base; + char *_attributes; + int hasOwnAttributes; }; @@ -568,50 +574,33 @@ struct __pyx_obj_6ctabix_asBed { }; -/* "ctabix.pxd":210 - * cdef Parser parser +/* "ctabix.pxd":182 + * cdef char * _filename * - * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< - * cdef FILE * infile - * cdef char * buffer + * cdef class TabixIterator: # <<<<<<<<<<<<<< + * cdef ti_iter_t iterator + * cdef tabix_t * tabixfile */ -struct __pyx_obj_6ctabix_tabix_inplace_iterator { +struct __pyx_obj_6ctabix_TabixIterator { PyObject_HEAD - struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab; - FILE *infile; - char *buffer; - size_t size; - struct __pyx_obj_6ctabix_Parser *parser; + ti_iter_t iterator; + tabix_t *tabixfile; }; -/* "ctabix.pxd":193 +/* "ctabix.pxd":202 * pass * - * cdef class asTuple(Parser): # <<<<<<<<<<<<<< + * cdef class asVCF(Parser): # <<<<<<<<<<<<<< * pass * */ -struct __pyx_obj_6ctabix_asTuple { +struct __pyx_obj_6ctabix_asVCF { struct __pyx_obj_6ctabix_Parser __pyx_base; }; -/* "ctabix.pyx":768 - * return self.__cnext__() - * - * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< - * '''iterate over ``infile``. - * - */ - -struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator { - PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *); -}; -static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator; - - /* "TabProxies.pxd":41 * ctypedef int uint64_t * @@ -644,18 +633,32 @@ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy { static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy; -/* "TabProxies.pxd":83 - * cdef update( self, char * buffer, size_t nbytes ) +/* "TabProxies.pxd":72 + * pass * - * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< + * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ -struct __pyx_vtabstruct_10TabProxies_VCFProxy { +struct __pyx_vtabstruct_10TabProxies_BedProxy { struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy; +static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy; + + +/* "ctabix.pyx":709 + * ## Iterators for parsing through unindexed files. + * ######################################################### + * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< + * '''iterate over ``infile``. + * + */ + +struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *); +}; +static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator; /* "TabProxies.pxd":60 @@ -673,32 +676,32 @@ struct __pyx_vtabstruct_10TabProxies_GTFProxy { static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy; -/* "TabProxies.pxd":72 - * pass +/* "ctabix.pyx":771 + * return self.__cnext__() * - * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< + * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<< + * '''iterate over ``infile``. * - * cdef: */ -struct __pyx_vtabstruct_10TabProxies_BedProxy { - struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; +struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator { + PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *); }; -static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy; +static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator; -/* "ctabix.pyx":706 - * ## Iterators for parsing through unindexed files. - * ######################################################### - * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<< - * '''iterate over ``infile``. +/* "TabProxies.pxd":83 + * cdef update( self, char * buffer, size_t nbytes ) + * + * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * + * cdef: */ -struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator { - PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *); +struct __pyx_vtabstruct_10TabProxies_VCFProxy { + struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base; }; -static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator; +static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy; #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -1196,20 +1199,21 @@ static char __pyx_k_34[] = "could not open '%s' for reading"; static char __pyx_k_36[] = "writing failed"; static char __pyx_k_40[] = "#"; static char __pyx_k_42[] = "No such file '%s'"; -static char __pyx_k_43[] = ".gz"; -static char __pyx_k_45[] = "Filename '%s.tbi' already exists, use *force* to overwrite"; -static char __pyx_k_47[] = "unknown preset '%s', valid presets are '%s'"; -static char __pyx_k_48[] = ","; -static char __pyx_k_49[] = "I/O operation on closed file."; -static char __pyx_k_52[] = "incomplete line at %s"; -static char __pyx_k_56[] = "tabix_generic_iterator"; -static char __pyx_k_57[] = "filename associated with this object."; -static char __pyx_k_58[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n "; -static char __pyx_k_59[] = "chromosome names"; -static char __pyx_k_60[] = "getfilesystemencoding"; -static char __pyx_k_63[] = "/ifs/devel/pysam/pysam/ctabix.pyx"; -static char __pyx_k_74[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n "; -static char __pyx_k_77[] = "tabix_inplace_iterator"; +static char __pyx_k_43[] = "neither preset nor seq_col,start_col and end_col given"; +static char __pyx_k_45[] = ".gz"; +static char __pyx_k_47[] = "Filename '%s.tbi' already exists, use *force* to overwrite"; +static char __pyx_k_49[] = "unknown preset '%s', valid presets are '%s'"; +static char __pyx_k_50[] = ","; +static char __pyx_k_51[] = "I/O operation on closed file."; +static char __pyx_k_54[] = "incomplete line at %s"; +static char __pyx_k_58[] = "tabix_generic_iterator"; +static char __pyx_k_59[] = "filename associated with this object."; +static char __pyx_k_60[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n "; +static char __pyx_k_61[] = "chromosome names"; +static char __pyx_k_62[] = "getfilesystemencoding"; +static char __pyx_k_65[] = "/home/andreas/devel/pysam/pysam/ctabix.pyx"; +static char __pyx_k_76[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n "; +static char __pyx_k_79[] = "tabix_inplace_iterator"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__r[] = "r"; @@ -1331,17 +1335,18 @@ static PyObject *__pyx_kp_s_42; static PyObject *__pyx_kp_s_43; static PyObject *__pyx_kp_s_45; static PyObject *__pyx_kp_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_52; -static PyObject *__pyx_n_s_56; +static PyObject *__pyx_kp_s_50; +static PyObject *__pyx_kp_s_51; +static PyObject *__pyx_kp_s_54; +static PyObject *__pyx_n_s_58; static PyObject *__pyx_kp_s_6; -static PyObject *__pyx_n_s_60; -static PyObject *__pyx_kp_s_63; +static PyObject *__pyx_n_s_62; +static PyObject *__pyx_kp_s_65; static PyObject *__pyx_kp_s_7; -static PyObject *__pyx_kp_s_74; -static PyObject *__pyx_n_s_77; +static PyObject *__pyx_kp_s_76; +static PyObject *__pyx_n_s_79; static PyObject *__pyx_kp_s_9; static PyObject *__pyx_n_s__IOError; static PyObject *__pyx_n_s__KeyError; @@ -1473,25 +1478,26 @@ static PyObject *__pyx_k_tuple_37; static PyObject *__pyx_k_tuple_38; static PyObject *__pyx_k_tuple_44; static PyObject *__pyx_k_tuple_46; -static PyObject *__pyx_k_tuple_50; -static PyObject *__pyx_k_tuple_51; +static PyObject *__pyx_k_tuple_48; +static PyObject *__pyx_k_tuple_52; static PyObject *__pyx_k_tuple_53; -static PyObject *__pyx_k_tuple_54; static PyObject *__pyx_k_tuple_55; -static PyObject *__pyx_k_tuple_61; -static PyObject *__pyx_k_tuple_64; +static PyObject *__pyx_k_tuple_56; +static PyObject *__pyx_k_tuple_57; +static PyObject *__pyx_k_tuple_63; static PyObject *__pyx_k_tuple_66; static PyObject *__pyx_k_tuple_68; static PyObject *__pyx_k_tuple_70; static PyObject *__pyx_k_tuple_72; -static PyObject *__pyx_k_tuple_75; -static PyObject *__pyx_k_codeobj_62; -static PyObject *__pyx_k_codeobj_65; +static PyObject *__pyx_k_tuple_74; +static PyObject *__pyx_k_tuple_77; +static PyObject *__pyx_k_codeobj_64; static PyObject *__pyx_k_codeobj_67; static PyObject *__pyx_k_codeobj_69; static PyObject *__pyx_k_codeobj_71; static PyObject *__pyx_k_codeobj_73; -static PyObject *__pyx_k_codeobj_76; +static PyObject *__pyx_k_codeobj_75; +static PyObject *__pyx_k_codeobj_78; /* "ctabix.pyx":19 * from cpython.version cimport PY_MAJOR_VERSION @@ -4319,6 +4325,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; int __pyx_t_3; + tabix_t *__pyx_t_4; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -4352,7 +4359,8 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T * * if tid < 0: */ - __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile; + __pyx_t_4 = __pyx_v_tabixfile->tabixfile; + __pyx_v_self->tabixfile = __pyx_t_4; /* "ctabix.pyx":293 * self.tabixfile = tabixfile.tabixfile @@ -4713,6 +4721,7 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; int __pyx_t_3; + tabix_t *__pyx_t_4; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -4746,7 +4755,8 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct * * self.iterator = ti_query(self.tabixfile, NULL, 0, 0) */ - __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile; + __pyx_t_4 = __pyx_v_tabixfile->tabixfile; + __pyx_v_self->tabixfile = __pyx_t_4; /* "ctabix.pyx":344 * self.tabixfile = tabixfile.tabixfile @@ -5576,6 +5586,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; int __pyx_t_3; + tabix_t *__pyx_t_4; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -5622,7 +5633,8 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct * * if tid < 0: */ - __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile; + __pyx_t_4 = __pyx_v_tabixfile->tabixfile; + __pyx_v_self->tabixfile = __pyx_t_4; /* "ctabix.pyx":530 * self.tabixfile = tabixfile.tabixfile @@ -6512,23 +6524,25 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel PyObject *__pyx_t_3 = NULL; int __pyx_t_4; int __pyx_t_5; - PyObject *__pyx_t_6 = NULL; + int __pyx_t_6; int __pyx_t_7; - PyObject *__pyx_t_8 = NULL; + int __pyx_t_8; PyObject *__pyx_t_9 = NULL; PyObject *__pyx_t_10 = NULL; - int __pyx_t_11; + PyObject *__pyx_t_11 = NULL; PyObject *__pyx_t_12 = NULL; - PyObject *__pyx_t_13 = NULL; + int __pyx_t_13; PyObject *__pyx_t_14 = NULL; - PyObject *(*__pyx_t_15)(PyObject *); - int32_t __pyx_t_16; - int32_t __pyx_t_17; + PyObject *__pyx_t_15 = NULL; + PyObject *__pyx_t_16 = NULL; + PyObject *(*__pyx_t_17)(PyObject *); int32_t __pyx_t_18; int32_t __pyx_t_19; int32_t __pyx_t_20; int32_t __pyx_t_21; - char *__pyx_t_22; + int32_t __pyx_t_22; + int32_t __pyx_t_23; + char *__pyx_t_24; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -6542,7 +6556,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel * * if not os.path.exists(filename): raise IOError("No such file '%s'" % filename) # <<<<<<<<<<<<<< * - * if not filename.endswith(".gz"): + * if preset == None and (seq_col == None or start_col == None or end_col == None): */ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); @@ -6585,32 +6599,84 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel /* "ctabix.pyx":655 * if not os.path.exists(filename): raise IOError("No such file '%s'" % filename) * - * if not filename.endswith(".gz"): # <<<<<<<<<<<<<< - * tabix_compress( filename, filename + ".gz", force = force ) - * os.unlink( filename ) + * if preset == None and (seq_col == None or start_col == None or end_col == None): # <<<<<<<<<<<<<< + * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) + * */ - __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__endswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_44), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); + __pyx_t_3 = PyObject_RichCompare(__pyx_v_preset, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - __pyx_t_4 = (!__pyx_t_5); + if (__pyx_t_5) { + __pyx_t_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (!__pyx_t_4) { + __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + if (!__pyx_t_6) { + __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_8 = __pyx_t_7; + } else { + __pyx_t_8 = __pyx_t_6; + } + __pyx_t_6 = __pyx_t_8; + } else { + __pyx_t_6 = __pyx_t_4; + } + __pyx_t_4 = __pyx_t_6; + } else { + __pyx_t_4 = __pyx_t_5; + } if (__pyx_t_4) { /* "ctabix.pyx":656 * + * if preset == None and (seq_col == None or start_col == None or end_col == None): + * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) # <<<<<<<<<<<<<< + * + * if not filename.endswith(".gz"): + */ + __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_44), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L4; + } + __pyx_L4:; + + /* "ctabix.pyx":658 + * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) + * + * if not filename.endswith(".gz"): # <<<<<<<<<<<<<< + * tabix_compress( filename, filename + ".gz", force = force ) + * os.unlink( filename ) + */ + __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__endswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_46), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_2); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; 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goto __pyx_L1_error;} + __pyx_t_4 = (!__pyx_t_5); + if (__pyx_t_4) { + __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); + __pyx_t_9 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; 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__pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + __pyx_t_6 = __pyx_t_5; } else { - __pyx_t_7 = __pyx_t_5; + __pyx_t_6 = __pyx_t_4; } - if (__pyx_t_7) { + if (__pyx_t_6) { - /* "ctabix.pyx":661 + /* "ctabix.pyx":664 * * if not force and os.path.exists(filename + ".tbi" ): * raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" ) # <<<<<<<<<<<<<< * * # columns (1-based) */ - __pyx_t_6 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_k_tuple_46), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_6); - __Pyx_Raise(__pyx_t_6, 0, 0, 0); - __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + __pyx_t_9 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_k_tuple_48), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + __Pyx_Raise(__pyx_t_9, 0, 0, 0); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L6; } - __pyx_L5:; + __pyx_L6:; - /* "ctabix.pyx":666 + /* "ctabix.pyx":669 * # preset-code, contig, start, end, metachar for commends, lines to ignore at beginning * # 0 is a missing column * preset2conf = { # <<<<<<<<<<<<<< * 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), */ - __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(((PyObject *)__pyx_t_6)); + __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(((PyObject *)__pyx_t_9)); - /* "ctabix.pyx":667 + /* "ctabix.pyx":670 * # 0 is a missing column * preset2conf = { * 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), # <<<<<<<<<<<<<< * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), * 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), */ - __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_int_0); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_0); @@ -6757,17 +6823,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_INCREF(__pyx_int_0); PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0); __Pyx_GIVEREF(__pyx_int_0); - if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__gff), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__gff), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":668 + /* "ctabix.pyx":671 * preset2conf = { * 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), # <<<<<<<<<<<<<< * 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), * 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ), */ - __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 668; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_int_65536); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_65536); @@ -6787,17 +6853,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_INCREF(__pyx_int_0); PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0); __Pyx_GIVEREF(__pyx_int_0); - if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__bed), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__bed), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":669 + /* "ctabix.pyx":672 * 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), * 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), # <<<<<<<<<<<<<< * 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ), * 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ), */ - __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_INCREF(__pyx_int_65536); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_65536); @@ -6817,17 +6883,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel __Pyx_INCREF(__pyx_int_0); PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0); __Pyx_GIVEREF(__pyx_int_0); - if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__psltbl), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__psltbl), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - /* "ctabix.pyx":670 + /* "ctabix.pyx":673 * 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), * 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), * 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ), # <<<<<<<<<<<<<< * 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ), * 'pileup': (3, 1, 2, 0, ord('#'), 0 ), */ - __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; 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/* "ctabix.pyx":782 + /* "ctabix.pyx":785 * if fd == -1: raise ValueError( "I/O operation on closed file." ) * self.infile = fdopen( fd, 'r') * if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<< @@ -7948,16 +8016,16 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct */ __pyx_t_2 = (__pyx_v_self->infile == NULL); if (__pyx_t_2) { - __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_54), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_56), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L4; } __pyx_L4:; - 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/* "ctabix.pyx":812 + /* "ctabix.pyx":815 * if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': * result = b * free(b) # <<<<<<<<<<<<<< @@ -8167,34 +8235,34 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob */ free(__pyx_v_b); - /* "ctabix.pyx":813 + /* "ctabix.pyx":816 * result = b * free(b) * raise ValueError( "incomplete line at %s" % result ) # <<<<<<<<<<<<<< * * # make sure that this goes fully through C */ - __pyx_t_5 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_5)); - __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_52), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; - __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_6)); __Pyx_GIVEREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0; - __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_6); __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; __Pyx_Raise(__pyx_t_6, 0, 0, 0); __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L8; } __pyx_L8:; - /* "ctabix.pyx":820 + /* "ctabix.pyx":823 * # the wrong memory is freed * # -1 to remove the new-line character * return self.parser(b, nbytes) # <<<<<<<<<<<<<< @@ -8202,11 +8270,11 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob * free(b) */ __Pyx_XDECREF(__pyx_r); - __pyx_t_6 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_6)); - __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_7); PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6)); __Pyx_GIVEREF(((PyObject *)__pyx_t_6)); @@ -8214,7 +8282,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob __Pyx_GIVEREF(__pyx_t_5); __pyx_t_6 = 0; __pyx_t_5 = 0; - __pyx_t_5 = PyObject_Call(((PyObject *)__pyx_v_self->parser), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_Call(((PyObject *)__pyx_v_self->parser), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0; __pyx_r = __pyx_t_5; @@ -8224,7 +8292,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob } __pyx_L4_break:; - /* "ctabix.pyx":822 + /* "ctabix.pyx":825 * return self.parser(b, nbytes) * * free(b) # <<<<<<<<<<<<<< @@ -8233,7 +8301,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob */ free(__pyx_v_b); - /* "ctabix.pyx":823 + /* "ctabix.pyx":826 * * free(b) * raise StopIteration # <<<<<<<<<<<<<< @@ -8241,7 +8309,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob * def __next__(self): */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -8268,7 +8336,7 @@ static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__(PyObject *__py return __pyx_r; } -/* "ctabix.pyx":825 +/* "ctabix.pyx":828 * raise StopIteration * * def __next__(self): # <<<<<<<<<<<<<< @@ -8285,7 +8353,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__next__", 0); - /* "ctabix.pyx":826 + /* "ctabix.pyx":829 * * def __next__(self): * return self.__cnext__() # <<<<<<<<<<<<<< @@ -8293,7 +8361,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o * class tabix_generic_iterator: */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; @@ -8343,16 +8411,16 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *_ case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--; else { - 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/* "ctabix.pyx":869 + /* "ctabix.pyx":872 * # create a copy * cpy = malloc(nbytes+1) * if cpy == NULL: raise MemoryError() # <<<<<<<<<<<<<< @@ -8730,12 +8798,12 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS */ __pyx_t_8 = (__pyx_v_cpy == NULL); if (__pyx_t_8) { - PyErr_NoMemory(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_NoMemory(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L9; } __pyx_L9:; - /* "ctabix.pyx":870 + /* "ctabix.pyx":873 * cpy = malloc(nbytes+1) * if cpy == NULL: raise MemoryError() * memcpy( cpy, b, nbytes+1) # <<<<<<<<<<<<<< @@ -8744,7 +8812,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS */ memcpy(__pyx_v_cpy, __pyx_v_b, (__pyx_v_nbytes + 1)); - /* "ctabix.pyx":872 + /* "ctabix.pyx":875 * memcpy( cpy, b, nbytes+1) * * return self.parser(cpy, nbytes) # <<<<<<<<<<<<<< @@ -8752,13 +8820,13 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS * raise StopIteration */ __Pyx_XDECREF(__pyx_r); - 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__pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_10); PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_2)); __Pyx_GIVEREF(((PyObject *)__pyx_t_2)); @@ -8766,7 +8834,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS __Pyx_GIVEREF(__pyx_t_9); __pyx_t_2 = 0; __pyx_t_9 = 0; - __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0; @@ -8777,7 +8845,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS } __pyx_L4_break:; - /* "ctabix.pyx":874 + /* "ctabix.pyx":877 * return self.parser(cpy, nbytes) * * raise StopIteration # <<<<<<<<<<<<<< @@ -8785,7 +8853,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS * # python version - required for python 2.7 */ __Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; @@ -8817,7 +8885,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_7next(PyObject *__pyx return __pyx_r; } -/* "ctabix.pyx":877 +/* "ctabix.pyx":880 * * # python version - required for python 2.7 * def next(self): # <<<<<<<<<<<<<< @@ -8835,7 +8903,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED P int __pyx_clineno = 0; __Pyx_RefNannySetupContext("next", 0); - /* "ctabix.pyx":878 + /* "ctabix.pyx":881 * # python version - required for python 2.7 * def next(self): * return self.__next__() # <<<<<<<<<<<<<< @@ -8843,9 +8911,9 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED P * def tabix_iterator( infile, parser ): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____next__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____next__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_r = __pyx_t_2; @@ -8895,11 +8963,11 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "tabix_iterator") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "tabix_iterator") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -8912,7 +8980,7 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("ctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -8923,7 +8991,7 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject return __pyx_r; } -/* "ctabix.pyx":880 +/* "ctabix.pyx":883 * return self.__next__() * * def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<< @@ -8942,7 +9010,7 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("tabix_iterator", 0); - /* "ctabix.pyx":882 + /* "ctabix.pyx":885 * def tabix_iterator( infile, parser ): * """return an iterator over all entries in a file.""" * return tabix_generic_iterator( infile, parser ) # <<<<<<<<<<<<<< @@ -8950,9 +9018,9 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_ * # used to be: isinstance( infile, file): */ __Pyx_XDECREF(__pyx_r); - 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__pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0; @@ -9026,9 +9094,9 @@ static PyMethodDef __pyx_methods_6ctabix_Tabixfile[] = { }; static struct PyGetSetDef __pyx_getsets_6ctabix_Tabixfile[] = { - {(char *)"filename", __pyx_getprop_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_57), 0}, - {(char *)"header", __pyx_getprop_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_58), 0}, - {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_59), 0}, + {(char *)"filename", __pyx_getprop_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_59), 0}, + {(char *)"header", __pyx_getprop_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_60), 0}, + {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_61), 0}, {0, 0, 0, 0, 0} }; @@ -10386,6 +10454,7 @@ static PyObject *__pyx_tp_new_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObj static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) { struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o; + PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); @@ -10396,6 +10465,7 @@ static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) { PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->parser); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } @@ -10592,6 +10662,7 @@ static PyObject *__pyx_tp_new_6ctabix_tabix_inplace_iterator(PyTypeObject *t, Py static void __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator(PyObject *o) { struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o; + PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); @@ -10602,6 +10673,7 @@ static void __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator(PyObject *o) { PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->parser); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } @@ -10798,7 +10870,9 @@ static PyObject *__pyx_tp_new_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObj static void __pyx_tp_dealloc_6ctabix_tabix_copy_iterator(PyObject *o) { struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o; + PyObject_GC_UnTrack(o); Py_CLEAR(p->parser); + PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } @@ -11021,17 +11095,18 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0}, {&__pyx_kp_s_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 1, 0}, {&__pyx_kp_s_47, __pyx_k_47, sizeof(__pyx_k_47), 0, 0, 1, 0}, - 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if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_iterator, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_iterator, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "ctabix.pyx":896 + /* "ctabix.pyx":899 * # return tabix_generic_iterator( infile, parser ) * * __all__ = ["tabix_index", # <<<<<<<<<<<<<< * "tabix_compress", * "Tabixfile", */ - __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_index)); PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tabix_index)); @@ -12160,10 +12257,10 @@ PyMODINIT_FUNC PyInit_ctabix(void) __Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_iterator)); PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__tabix_iterator)); __Pyx_GIVEREF(((PyObject *)__pyx_n_s__tabix_iterator)); - __Pyx_INCREF(((PyObject *)__pyx_n_s_77)); - PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_77)); - __Pyx_GIVEREF(((PyObject *)__pyx_n_s_77)); - if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_INCREF(((PyObject *)__pyx_n_s_79)); + PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_79)); + __Pyx_GIVEREF(((PyObject *)__pyx_n_s_79)); + if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; /* "ctabix.pyx":1 @@ -13285,6 +13382,10 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { else return (int32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { + #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); + #else int32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 @@ -13304,6 +13405,7 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { if (likely(!ret)) return val; } + #endif return (int32_t)-1; } } diff --git a/pysam/ctabix.pyx b/pysam/ctabix.pyx index a522676..6a19541 100644 --- a/pysam/ctabix.pyx +++ b/pysam/ctabix.pyx @@ -652,6 +652,9 @@ def tabix_index( filename, if not os.path.exists(filename): raise IOError("No such file '%s'" % filename) + if preset == None and (seq_col == None or start_col == None or end_col == None): + raise ValueError("neither preset nor seq_col,start_col and end_col given" ) + if not filename.endswith(".gz"): tabix_compress( filename, filename + ".gz", force = force ) os.unlink( filename ) diff --git a/pysam/cvcf.c b/pysam/cvcf.c index 6caaba0..6243139 100644 --- a/pysam/cvcf.c +++ b/pysam/cvcf.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.16 on Mon Nov 19 08:44:41 2012 */ +/* Generated by Cython 0.16 on Tue Nov 6 12:17:11 2012 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -461,8 +461,8 @@ struct __pyx_obj_10TabProxies_TupleProxy { }; -/* "TabProxies.pxd":69 - * cdef char * getAttributes( self ) +/* "TabProxies.pxd":68 + * cdef int getMaxFields( self, size_t nbytes ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass @@ -473,7 +473,7 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy { }; -/* "TabProxies.pxd":72 +/* "TabProxies.pxd":71 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -519,7 +519,7 @@ struct __pyx_obj_4cvcf_VCFRecord { }; -/* "TabProxies.pxd":83 +/* "TabProxies.pxd":82 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -753,8 +753,8 @@ struct __pyx_vtabstruct_10TabProxies_TupleProxy { static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy; -/* "TabProxies.pxd":69 - * cdef char * getAttributes( self ) +/* "TabProxies.pxd":68 + * cdef int getMaxFields( self, size_t nbytes ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass @@ -767,7 +767,7 @@ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy { static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy; -/* "TabProxies.pxd":83 +/* "TabProxies.pxd":82 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -805,7 +805,6 @@ static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ct struct __pyx_vtabstruct_10TabProxies_GTFProxy { struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base; - char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *); }; static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy; @@ -824,7 +823,7 @@ struct __pyx_vtabstruct_4cvcf_VCFRecord { static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord; -/* "TabProxies.pxd":72 +/* "TabProxies.pxd":71 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< @@ -1468,7 +1467,7 @@ static char __pyx_k_125[] = "Invalid error string: %s"; static char __pyx_k_126[] = "needs to be checked"; static char __pyx_k_128[] = "[|/\\\\]"; static char __pyx_k_130[] = "^[ACGTN]+$"; -static char __pyx_k_134[] = "/ifs/devel/pysam/pysam/cvcf.pyx"; +static char __pyx_k_134[] = "/home/andreas/devel/pysam/pysam/cvcf.pyx"; static char __pyx_k_137[] = "id numbertype number type description missingvalue"; static char __pyx_k_139[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier"; static char __pyx_k_140[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string"; @@ -26499,12 +26498,12 @@ PyMODINIT_FUNC PyInit_cvcf(void) __pyx_vtabptr_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_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 = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ diff --git a/pysam/version.py b/pysam/version.py index 6755f3d..7e6b192 100644 --- a/pysam/version.py +++ b/pysam/version.py @@ -1,6 +1,6 @@ # pysam versioning information -__version__ = "0.7" +__version__ = "0.7.1" __samtools_version__ = "0.1.18" diff --git a/setup.cfg b/setup.cfg index b9711b8..81d163a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,8 +1,8 @@ [bdist_rpm] -doc_files = README doc/*.html ChangeLog vendor = TDB -packager = TDB +doc_files = README doc/*.html ChangeLog distribution-name = Red Hat Linux +packager = TDB requires = python [egg_info] diff --git a/setup.py b/setup.py index 979b936..a1b8de8 100644 --- a/setup.py +++ b/setup.py @@ -114,14 +114,30 @@ if len(sys.argv) >= 2 and sys.argv[1] == "refresh": sys.exit(0) - - from distribute_setup import use_setuptools use_setuptools() from setuptools import Extension, setup -from Cython.Distutils import build_ext +####################################################### +####################################################### +try: + from Cython.Distutils import build_ext +except ImportError: + # no Cython available - use existing C code + cmdclass = { } + csamtools_sources = [ "pysam/csamtools.c" ] + tabix_sources = [ "pysam/tabix.c" ] + tabproxies_sourcess = ["pysam/TabProxies.c" ] + cvcf_sources = ["pysam/cvcf.c" ] +else: + cmdclass = { 'build_ext' : build_ext } + csamtools_sources = [ "pysam/csamtools.pyx" ] + tabix_sources = [ "pysam/ctabix.pyx" ] + tabproxies_sources = ["pysam/TabProxies.pyx" ] + cvcf_sources = ["pysam/cvcf.pyx" ] + +####################################################### classifiers = """ Development Status :: 2 - Alpha Operating System :: MacOS :: MacOS X @@ -135,6 +151,8 @@ Topic :: Scientific/Engineering Topic :: Scientific/Engineering :: Bioinformatics """ +####################################################### +## Windows compatibility if platform.system()=='Windows': include_os = ['win32'] os_c_files = ['win32/getopt.c'] @@ -142,9 +160,10 @@ else: include_os = [] os_c_files = [] +####################################################### samtools = Extension( - "csamtools", # name of extension - [ "pysam/csamtools.pyx" ] +\ + "csamtools", + csamtools_sources +\ [ "pysam/%s" % x for x in ( "pysam_util.c", )] +\ glob.glob( os.path.join( "samtools", "*.pysam.c" )) +\ @@ -159,8 +178,8 @@ samtools = Extension( ) tabix = Extension( - "ctabix", # name of extension - [ "pysam/ctabix.pyx", ] +\ + "ctabix", + tabix_sources +\ [ "pysam/%s" % x for x in ( "tabix_util.c", )] +\ os_c_files + \ glob.glob( os.path.join( "tabix", "*.pysam.c" ) ), @@ -173,8 +192,8 @@ tabix = Extension( ) tabproxies = Extension( - "TabProxies", # name of extension - [ "pysam/TabProxies.pyx", ] + os_c_files, + "TabProxies", + tabproxies_sources + os_c_files, library_dirs=[], include_dirs= include_os, libraries=[ "z", ], @@ -182,8 +201,8 @@ tabproxies = Extension( ) cvcf = Extension( - "cvcf", # name of extension - [ "pysam/cvcf.pyx", ] + os_c_files, + "cvcf", + cvcf_sources + os_c_files, library_dirs=[], include_dirs= ["tabix",] + include_os, libraries=[ "z", ], @@ -207,7 +226,7 @@ metadata = { # cython larger that 0.16 for yield support 'requires' : ['cython (>=0.16)'], 'ext_modules': [samtools, tabix, tabproxies, cvcf ], - 'cmdclass' : {'build_ext': build_ext}, + 'cmdclass' : cmdclass, 'install_requires' : ['cython>=0.12.1',], # do not pack in order to permit linking to csamtools.so 'zip_safe' :False, diff --git a/tests/example_btag.bam b/tests/example_btag.bam new file mode 100644 index 0000000..7cd5c0c Binary files /dev/null and b/tests/example_btag.bam differ diff --git a/tests/pysam_test.py b/tests/pysam_test.py index 3407182..c8acf83 100755 --- a/tests/pysam_test.py +++ b/tests/pysam_test.py @@ -891,6 +891,16 @@ class TestHeaderBam(TestHeaderSam): self.samfile=pysam.Samfile( "ex3.bam","rb" ) +class TestHeader1000Genomes( unittest.TestCase ): + + bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam" + + def testRead( self ): + + f = pysam.Samfile( self.bamfile, "rb" ) + data = f.header.copy() + self.assertTrue( data ) + class TestUnmappedReads(unittest.TestCase): def testSAM(self):