[med-svn] [pysam] 07/13: Imported Upstream version 0.7.4
Charles Plessy
plessy at alioth.debian.org
Fri Aug 9 09:47:30 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository pysam.
commit 356c1c89be26c412e68323cc506e42159ff4b74d
Author: Charles Plessy <plessy at debian.org>
Date: Fri Aug 9 18:34:36 2013 +0900
Imported Upstream version 0.7.4
---
PKG-INFO | 2 +-
pysam.egg-info/PKG-INFO | 2 +-
pysam.egg-info/SOURCES.txt | 7 +-
pysam/TabProxies.c | 4 +-
pysam/VCF.py | 1087 ---
pysam/__init__.py | 9 +-
pysam/alternatives.py | 82 -
pysam/csamtools.c |22245 +++++++++++++++++++-------------------------
pysam/ctabix.c | 1300 ++-
pysam/cvcf.c | 5735 +++++-------
pysam/version.py | 2 +-
setup.cfg | 4 +-
setup.py | 12 +-
13 files changed, 12431 insertions(+), 18060 deletions(-)
diff --git a/PKG-INFO b/PKG-INFO
index 905bd25..c527383 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.3
+Version: 0.7.4
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 905bd25..c527383 100644
--- a/pysam.egg-info/PKG-INFO
+++ b/pysam.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.3
+Version: 0.7.4
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 8a914d5..718c4d2 100644
--- a/pysam.egg-info/SOURCES.txt
+++ b/pysam.egg-info/SOURCES.txt
@@ -10,9 +10,7 @@ pysam/Pileup.py
pysam/TabProxies.c
pysam/TabProxies.pxd
pysam/TabProxies.pyx
-pysam/VCF.py
pysam/__init__.py
-pysam/alternatives.py
pysam/csamtools.c
pysam/csamtools.pxd
pysam/csamtools.pyx
@@ -33,6 +31,8 @@ pysam.egg-info/dependency_links.txt
pysam.egg-info/not-zip-safe
pysam.egg-info/requires.txt
pysam.egg-info/top_level.txt
+pysam/include/__init__.py
+samtools/__init__.py
samtools/bam.c.pysam.c
samtools/bam.h
samtools/bam2bcf.c.pysam.c
@@ -87,6 +87,7 @@ samtools/sam_header.h
samtools/sam_view.c.pysam.c
samtools/sample.c.pysam.c
samtools/sample.h
+samtools/bcftools/__init__.py
samtools/bcftools/bcf.c.pysam.c
samtools/bcftools/bcf.h
samtools/bcftools/bcf2qcall.c.pysam.c
@@ -105,9 +106,11 @@ samtools/bcftools/vcf.c.pysam.c
samtools/misc/md5.c.pysam.c
samtools/misc/md5.h
samtools/misc/seqtk.c.pysam.c
+samtools/win32/__init__.py
samtools/win32/xcurses.h
samtools/win32/zconf.h
samtools/win32/zlib.h
+tabix/__init__.py
tabix/bam_endian.h
tabix/bedidx.c
tabix/bedidx.c.pysam.c
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'] = '<none>'
- if not data['type'] and not data['number']:
- # fine, ##filter format
- return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
- if not data['type'] in ["Integer","Float","Character","String","Flag"]:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- # I would like a missing-value field, but it isn't there
- if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
- else: data['missing'] = '.'
- if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- try:
- n = int(data['number'])
- t = self.NT_NUMBER
- except ValueError:
- n = -1
- if data['number'] == '.': t = self.NT_UNKNOWN
- elif data['number'] == '#alleles': t = self.NT_ALLELES
- elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
- elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
- elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
- else:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
-
-
- def format_format( self, fmt, filter=False ):
- values = [('ID',fmt.id)]
- if fmt.number != None and not filter:
- if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
- elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
- elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
- elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
- elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
- elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
- else:
- raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
- values.append( ('Number',nmb) )
- values.append( ('Type', fmt.type) )
- values.append( ('Description', '"' + fmt.description + '"') )
- if self._version == 33:
- format = ",".join(v for k,v in values)
- else:
- format = "<" + (",".join( "%s=%s" % (k,v) for (k,v) in values )) + ">"
- return format
-
- def get_expected(self, format, formatdict, alt):
- fmt = formatdict[format]
- if fmt.numbertype == self.NT_UNKNOWN: return -1
- if fmt.numbertype == self.NT_NUMBER: return fmt.number
- if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
- if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
- if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
- if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
- return 0
-
-
- def _add_definition(self, formatdict, key, data, line ):
- if key in formatdict: return
- self.error(line,self.ERROR_UNKNOWN_KEY,key)
- if data == None:
- formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
- return
- if data == []: data = [""] # unsure what type -- say string
- if type(data[0]) == type(0.0):
- formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
- return
- if type(data[0]) == type(0):
- formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
- return
- formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
-
-
- # todo: trim trailing missing values
- def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
- output, sdata = [], []
- if type(data) == type([]): # for FORMAT field, make data with dummy values
- d = {}
- for k in data: d[k] = []
- data = d
- # convert missing values; and silently add definitions if required
- for k in data:
- self._add_definition( format, k, data[k], "(output)" )
- for idx,v in enumerate(data[k]):
- if v == format[k].missingvalue: data[k][idx] = "."
- # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
- for k in data:
- if k != 'GT': sdata.append( (k,data[k]) )
- sdata.sort()
- if 'GT' in data:
- sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
- for k,v in sdata:
- if v == []: v = None
- if key and value:
- if v != None: output.append( k+"="+','.join(map(str,v)) )
- else: output.append( k )
- elif key: output.append(k)
- elif value:
- if v != None: output.append( ','.join(map(str,v)) )
- else: output.append( "." ) # should not happen
- # snip off trailing missing data
- while len(output) > 1:
- last = output[-1].replace(',','').replace('.','')
- if len(last)>0: break
- output = output[:-1]
- return separator.join(output)
-
-
- def enter_default_format(self):
- for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
- FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
- FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
- FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
- FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.')]:
- if f.id not in self._format:
- self._format[f.id] = f
-
- def parse_header( self, line ):
- assert line.startswith('##')
- elts = line[2:].split('=')
- key = elts[0].strip()
- value = '='.join(elts[1:]).strip()
- if key == "fileformat":
- if value == "VCFv3.3":
- self._version = 33
- elif value == "VCFv4.0":
- self._version = 40
- elif value == "VCFv4.1":
- 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<seq> and D<num>
- have_deletions = True
- try:
- l = int(a[1:]) # throws ValueError if sequence
- if len(ref) < l: # add to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[l:] # new deletion, deleting pos...pos+l
- except ValueError:
- s = a[1:]
- if len(ref) < len(s): # add Ns to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
- if not s.endswith(addns) and addns != 'N'*len(addns):
- self.error(line,self.V33_UNMATCHED_DELETION,
- "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[len(s):] # new deletion, deleting from pos
- else:
- self.error(line,self.V33_BAD_ALLELE)
- newalts.append(a)
- alt = newalts
- # deletion alleles exist, add dummy 1st reference allele, and account for leading base
- if have_deletions:
- if pos == 0:
- # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
- addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
- ref += addn
- alt = [allele+addn for allele in alt]
- else:
- addn = get_sequence(chrom,pos-1,pos,self._reference)
- ref = addn + ref
- alt = [addn + allele for allele in alt]
- pos -= 1
- else:
- # format v4.0 -- just check for nucleotides
- for allele in alt:
- if not alleleRegEx.match(allele):
- self.error(line,self.V40_BAD_ALLELE,allele)
-
- # check for leading nucleotide in indel calls
- for allele in alt:
- if len(allele) != len(ref):
- if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
- if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
- self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
-
- # trim trailing bases in alleles
- for i in range(1,min(len(ref),min(map(len,alt)))):
- if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
- break
- ref, alt = ref[:-1], [allele[:-1] for allele in alt]
-
- # left-align alleles, if a reference is available
- if self._leftalign and self._reference:
- while left < pos:
- movable = True
- for allele in alt:
- if len(allele) > len(ref):
- longest, shortest = allele, ref
- else:
- longest, shortest = ref, allele
- if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
- movable = False
- if longest[-1].upper() != longest[len(shortest)-1].upper():
- movable = False
- if not movable:
- break
- ref = ref[:-1]
- alt = [allele[:-1] for allele in alt]
- if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
- ref = faref_leftflank[pos-left-1] + ref
- alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
- pos -= 1
-
- # parse sample columns
- samples = []
- for sample in cols[9:]:
- dict = {}
- values = sample.split(':')
- if len(values) > len(format):
- self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
- for idx in range(len(format)):
- expected = self.get_expected(format[idx], self._format, alt)
- if idx < len(values): value = values[idx]
- else:
- if expected == -1: value = "."
- else: value = ",".join(["."]*expected)
- dict[format[idx]] = self.parse_formatdata(format[idx], value, self._format, line)
- if expected != -1 and len(dict[format[idx]]) != expected:
- self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
- "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
- if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
- dict[format[idx]] = dict[format[idx]][:expected]
- samples.append( dict )
-
- # done
- d = {'chrom':chrom,
- 'pos':pos, # return 0-based position
- 'id':id,
- 'ref':ref,
- 'alt':alt,
- 'qual':qual,
- 'filter':filter,
- 'info':info,
- 'format':format}
- for key,value in zip(self._samples,samples):
- d[key] = value
-
- return d
-
-
- def write_data(self, stream, data):
- required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
- for k in required:
- if k not in data: raise ValueError("Required key %s not found in data" % str(k))
- if data['alt'] == []: alt = "."
- else: alt = ",".join(data['alt'])
- if data['filter'] == None: filter = "."
- elif data['filter'] == []:
- if self._version == 33: filter = "0"
- else: filter = "PASS"
- else: filter = ';'.join(data['filter'])
- if data['qual'] == -1: qual = "."
- else: qual = str(data['qual'])
-
- output = [data['chrom'],
- str(data['pos']+1), # change to 1-based position
- data['id'],
- data['ref'],
- alt,
- qual,
- filter,
- self.format_formatdata( data['info'], self._info, separator=";" ),
- self.format_formatdata( data['format'], self._format, value=False ) ]
-
- for s in self._samples:
- output.append( self.format_formatdata( data[s], self._format, key=False ) )
-
- stream.write( "\t".join(output) + "\n" )
-
- def _parse_header(self, stream):
- self._lineno = 0
- for line in stream:
- self._lineno += 1
- if line.startswith('##'):
- self.parse_header( line.strip() )
- elif line.startswith('#'):
- self.parse_heading( line.strip() )
- self.enter_default_format()
- else:
- break
- return line
-
- def _parse(self, line, stream):
- if len(line.strip()) > 0:
- d = self.parse_data( line.strip() )
- if d: yield d
- for line in stream:
- self._lineno += 1
- if self._lines and self._lineno > self._lines: raise StopIteration
- d = self.parse_data( line.strip() )
- if d: yield d
-
- ######################################################################################################
- #
- # API follows
- #
- ######################################################################################################
-
- def getsamples(self):
- """ List of samples in VCF file """
- return self._samples
-
- def setsamples(self,samples):
- """ List of samples in VCF file """
- self._samples = samples
-
- def getheader(self):
- """ List of header key-value pairs (strings) """
- return self._header
-
- def setheader(self,header):
- """ List of header key-value pairs (strings) """
- self._header = header
-
- def getinfo(self):
- """ Dictionary of ##INFO tags, as VCF.FORMAT values """
- return self._info
-
- def setinfo(self,info):
- """ Dictionary of ##INFO tags, as VCF.FORMAT values """
- self._info = info
-
- def getformat(self):
- """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
- return self._format
-
- def setformat(self,format):
- """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
- self._format = format
-
- def getfilter(self):
- """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
- return self._filter
-
- def setfilter(self,filter):
- """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
- self._filter = filter
-
- def setversion(self, version):
- if version 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<seq> and D<num>
- have_deletions = True
- try:
- l = int(a[1:]) # throws ValueError if sequence
- if len(ref) < l: # add to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[l:] # new deletion, deleting pos...pos+l
- except ValueError:
- s = a[1:]
- if len(ref) < len(s): # add Ns to reference if necessary
- addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
- if not s.endswith(addns) and addns != 'N'*len(addns):
- self.error(line,self.V33_UNMATCHED_DELETION,
- "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
- ref += addns
- for i,na in enumerate(newalts): newalts[i] = na+addns
- a = ref[len(s):] # new deletion, deleting from pos
- else:
- self.error(line,self.V33_BAD_ALLELE)
- newalts.append(a)
- alt = newalts
- # deletion alleles exist, add dummy 1st reference allele, and account for leading base
- if have_deletions:
- if pos == 0:
- # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
- addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
- ref += addn
- alt = [allele+addn for allele in alt]
- else:
- addn = get_sequence(chrom,pos-1,pos,self._reference)
- ref = addn + ref
- alt = [addn + allele for allele in alt]
- pos -= 1
- else:
- # format v4.0 -- just check for nucleotides
- for allele in alt:
- if not alleleRegEx.match(allele):
- self.error(line,self.V40_BAD_ALLELE,allele)
-
-
- # check for leading nucleotide in indel calls
- for allele in alt:
- if len(allele) != len(ref):
- if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
- if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
- self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
-
- # trim trailing bases in alleles
- for i in range(1,min(len(ref),min(map(len,alt)))):
- if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
- break
- ref, alt = ref[:-1], [allele[:-1] for allele in alt]
-
- # left-align alleles, if a reference is available
- if self._leftalign and self._reference:
- while left < pos:
- movable = True
- for allele in alt:
- if len(allele) > len(ref):
- longest, shortest = allele, ref
- else:
- longest, shortest = ref, allele
- if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
- movable = False
- if longest[-1].upper() != longest[len(shortest)-1].upper():
- movable = False
- if not movable:
- break
- ref = ref[:-1]
- alt = [allele[:-1] for allele in alt]
- if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
- ref = faref_leftflank[pos-left-1] + ref
- alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
- pos -= 1
-
-
-
-
diff --git a/pysam/__init__.py b/pysam/__init__.py
index e1d87ee..7e36c08 100644
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -127,8 +127,15 @@ __all__ = \
from pysam.version import __version__, __samtools_version__
+###########################################################
+# Utility functions for compilation
def get_include():
- return [os.path.abspath(os.path.join(os.path.dirname(__file__), 'include'))]
+ '''return a list of include directories.'''
+ dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
+ return [ dirname,
+ os.path.join(dirname, 'include', 'samtools'),
+ os.path.join(dirname, 'include', 'tabix') ]
def get_defines():
+ '''return a list of defined compilation parameters.'''
return [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')]
diff --git a/pysam/alternatives.py b/pysam/alternatives.py
deleted file mode 100644
index fd76802..0000000
--- a/pysam/alternatives.py
+++ /dev/null
@@ -1,82 +0,0 @@
-# This file contains an alternative implementation
-# to call samtools functions. These are direct calls.
-# Plus: less overhead
-# Minus: more trouble in maintaining
-
-#in csamtools.pxd
- # samtools toolkit functions
- ctypedef int (*pysam_samtools_f)(int argc, char *argv[])
-
- int bam_taf2baf(int argc, char *argv[])
- int bam_pileup(int argc, char *argv[])
- int bam_merge(int argc, char *argv[])
- int bam_index(int argc, char *argv[])
- int bam_sort(int argc, char *argv[])
- int bam_tview_main(int argc, char *argv[])
- int bam_mating(int argc, char *argv[])
- int bam_rmdup(int argc, char *argv[])
- int bam_rmdupse(int argc, char *argv[])
- int bam_flagstat(int argc, char *argv[])
- int bam_fillmd(int argc, char *argv[])
- int main_samview(int argc, char *argv[])
- int main_import(int argc, char *argv[])
- int faidx_main(int argc, char *argv[])
- int glf3_view_main(int argc, char *argv[])
-
-
-## Alternative code in csamtools.pyx
-cdef class SamtoolsWrapper:
- '''generic wrapper around samtools functions'''
- cdef pysam_samtools_f f
-
- def __init__(self): self.f = NULL
-
- def call(self, *args ):
-
- if self.f == NULL: raise NotImplementedError("invalid call to base class" )
-
- cdef char ** cargs
- cdef int i, n, retval
- n = len(args)
- # allocate one more for first (dummy) argument (contains command)
- cargs = <char**>calloc( n+1, sizeof( char *) )
- cargs[0] = "method"
- for i from 0 <= i < n:
- cargs[i+1] = args[i]
- for i from 0 <= i < n+1:
- print cargs[i]
- retval = self.f(n+1, cargs)
- free( cargs )
- return retval
-
-cdef class SamtoolsWrapperImport( SamtoolsWrapper ):
- def __init__(self): self.f = main_import
-cdef class SamtoolsWrapperPileup( SamtoolsWrapper ):
- def __init__(self): self.f = bam_pileup
-cdef class SamtoolsWrapperMerge( SamtoolsWrapper ):
- def __init__(self): self.f = bam_merge
-cdef class SamtoolsWrapperSort( SamtoolsWrapper ):
- def __init__(self): self.f = bam_sort
-cdef class SamtoolsWrapperIndex( SamtoolsWrapper ):
- def __init__(self): self.f = bam_index
-cdef class SamtoolsWrapperFaidx( SamtoolsWrapper ):
- def __init__(self): self.f = faidx_main
-cdef class SamtoolsWrapperFixMate( SamtoolsWrapper ):
- def __init__(self): self.f = bam_mating
-cdef class SamtoolsWrapperRmDup( SamtoolsWrapper ):
- def __init__(self): self.f = bam_rmdup
-cdef class SamtoolsWrapperRmDupSe( SamtoolsWrapper ):
- def __init__(self): self.f = bam_rmdupse
-cdef class SamtoolsWrapperGlf3Viwen( SamtoolsWrapper ):
- def __init__(self): self.f = glf3_view_main
-cdef class SamtoolsWrapperFlagStat( SamtoolsWrapper ):
- def __init__(self): self.f = bam_flagstat
-cdef class SamtoolsWrapperFillMd( SamtoolsWrapper ):
- def __init__(self): self.f = bam_fillmd
-cdef class SamtoolsWrapperCalMd( SamtoolsWrapper ):
- def __init__(self): self.f = bam_fillmd
-
-automatic creation of these functions does not work
-due to pyrex/cython
-
-def sort( *args, **kwargs ): return SamtoolsWrapperSort().call(*args, **kwargs)
diff --git a/pysam/csamtools.c b/pysam/csamtools.c
index e79d3c8..35b4522 100644
--- a/pysam/csamtools.c
+++ b/pysam/csamtools.c
@@ -1,16 +1,16 @@
-/* Generated by Cython 0.17.2 on Wed Jan 23 09:18:14 2013 */
+/* 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 <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
+
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -22,47 +22,36 @@
#define __fastcall
#endif
#endif
+
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
+
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
+
+#if PY_VERSION_HEX < 0x02040000
+ #define METH_COEXIST 0
+ #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
+ #define PyDict_Contains(d,o) PySequence_Contains(d,o)
#endif
+
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
+ #define 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"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -70,6 +59,7 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
+
typedef struct {
void *buf;
PyObject *obj;
@@ -83,6 +73,7 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
+
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -92,44 +83,24 @@
#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
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
+
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -137,6 +108,7 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -155,6 +127,7 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -162,7 +135,9 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -179,9 +154,11 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
+
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -190,6 +167,16 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#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)
@@ -208,9 +195,11 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -220,6 +209,7 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -228,15 +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"
@@ -249,8 +230,8 @@
#define _USE_MATH_DEFINES
#endif
#include <math.h>
-#define __PYX_HAVE__pysam__csamtools
-#define __PYX_HAVE_API__pysam__csamtools
+#define __PYX_HAVE__csamtools
+#define __PYX_HAVE_API__csamtools
#include "string.h"
#include "stdlib.h"
#include "math.h"
@@ -294,7 +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
@@ -318,12 +299,8 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
@@ -351,43 +328,50 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"csamtools.pyx",
- "type.pxd",
"bool.pxd",
"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_obj_5pysam_9csamtools_IteratorRow;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs;
-struct __pyx_obj_5pysam_9csamtools_Samfile;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection;
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
-struct __pyx_obj_5pysam_9csamtools_Fastafile;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
-struct __pyx_obj_5pysam_9csamtools_IteratorColumn;
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion;
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAll;
-struct __pyx_obj_5pysam_9csamtools_IndexedReads;
-struct __pyx_obj_5pysam_9csamtools_SNPCall;
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr;
-struct __pyx_obj_5pysam_9csamtools_AlignedRead;
-struct __pyx_obj_5pysam_9csamtools_PileupProxy;
-struct __pyx_obj_5pysam_9csamtools_PileupRead;
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs;
-struct __pyx_t_5pysam_9csamtools___iterdata;
-typedef struct __pyx_t_5pysam_9csamtools___iterdata __pyx_t_5pysam_9csamtools___iterdata;
-struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData;
-struct __pyx_t_5pysam_9csamtools_MateData;
-typedef struct __pyx_t_5pysam_9csamtools_MateData __pyx_t_5pysam_9csamtools_MateData;
-
-/* "pysam/csamtools.pxd":394
+struct __pyx_Generator_object;
+struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr;
+struct __pyx_obj_9csamtools_IteratorRow;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs;
+struct __pyx_obj_9csamtools_IteratorRowAll;
+struct __pyx_obj_9csamtools_PileupProxy;
+struct __pyx_obj_9csamtools_AlignedRead;
+struct __pyx_obj_9csamtools_Fastafile;
+struct __pyx_obj_9csamtools_IteratorRowSelection;
+struct __pyx_obj_9csamtools_IteratorColumn;
+struct __pyx_obj_9csamtools_IteratorColumnAllRefs;
+struct __pyx_obj_9csamtools_IteratorRowRegion;
+struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_9csamtools_Samfile;
+struct __pyx_obj_9csamtools_SNPCall;
+struct __pyx_obj_9csamtools_IndexedReads;
+struct __pyx_obj_9csamtools_IteratorColumnRegion;
+struct __pyx_obj_9csamtools_PileupRead;
+struct __pyx_t_9csamtools___iterdata;
+typedef struct __pyx_t_9csamtools___iterdata __pyx_t_9csamtools___iterdata;
+struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData;
+struct __pyx_t_9csamtools_MateData;
+typedef struct __pyx_t_9csamtools_MateData __pyx_t_9csamtools_MateData;
+
+/* "csamtools.pxd":394
* # Utility types
*
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
* samfile_t * samfile
* bam_iter_t iter
*/
-struct __pyx_t_5pysam_9csamtools___iterdata {
+struct __pyx_t_9csamtools___iterdata {
samfile_t *samfile;
bam_iter_t iter;
faidx_t *fastafile;
@@ -396,229 +380,266 @@ struct __pyx_t_5pysam_9csamtools___iterdata {
int seq_len;
};
-/* "pysam/csamtools.pxd":523
+/* "csamtools.pxd":523
* cdef char * getSequence( self )
* cdef setMask( self, mask )
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
* int tid,
* int start,
*/
-struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData {
+struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData {
int __pyx_n;
int reopen;
};
-/* "pysam/csamtools.pyx":518
+/* "csamtools.pyx":518
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
* char * name
* bam1_t * mate
*/
-struct __pyx_t_5pysam_9csamtools_MateData {
+struct __pyx_t_9csamtools_MateData {
char *name;
bam1_t *mate;
uint32_t flag;
};
-/* "pysam/csamtools.pxd":464
+/* "csamtools.pyx":140
+ * cdef char* CODE2CIGAR= "MIDNSHP=X"
+ * if IS_PYTHON3:
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
+ */
+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;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "csamtools.pxd":464
* cdef uint32_t _is_tail
*
* cdef class IteratorRow: # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRow {
+struct __pyx_obj_9csamtools_IteratorRow {
PyObject_HEAD
};
-/* "pysam/csamtools.pxd":487
+/* "csamtools.pxd":487
* cdef int cnext(self)
*
* cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
* cdef Samfile samfile
* cdef int tid
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+struct __pyx_obj_9csamtools_IteratorRowAllRefs {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
int tid;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *rowiter;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
};
-/* "pysam/csamtools.pxd":420
- * cdef bam1_t * _delegate
+/* "csamtools.pxd":480
+ * cdef int cnext(self)
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to samfile
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_Samfile {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtab;
- char *_filename;
- samfile_t *samfile;
- bam_index_t *index;
- int isbam;
- int isstream;
- int isremote;
+struct __pyx_obj_9csamtools_IteratorRowAll {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
bam1_t *b;
- char *mode;
- int64_t start_offset;
+ samfile_t *fp;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":492
- * cdef IteratorRowRegion rowiter
+/* "csamtools.pxd":449
+ * cdef char * _getrname( self, int tid )
*
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef int current_pos
+ * cdef class PileupProxy: # <<<<<<<<<<<<<<
+ * cdef bam_pileup1_t ** plp
+ * cdef int tid
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtab;
- bam1_t *b;
- int current_pos;
- samfile_t *fp;
- PyObject *positions;
- int owns_samfile;
+struct __pyx_obj_9csamtools_PileupProxy {
+ PyObject_HEAD
+ bam_pileup1_t **plp;
+ int tid;
+ int pos;
+ int n_pu;
};
-/* "pysam/csamtools.pyx":142
- * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
- * else:
- * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
- * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
+/* "csamtools.pxd":415
+ * cdef char * _fetch( self, char * reference, int start, int end, int * length )
+ *
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
*
+ * # object that this AlignedRead represents
*/
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
+struct __pyx_obj_9csamtools_AlignedRead {
PyObject_HEAD
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+ bam1_t *_delegate;
};
-/* "pysam/csamtools.pxd":408
+/* "csamtools.pxd":408
* # Note: need to declare all C fields and methods here
* #
* cdef class Fastafile: # <<<<<<<<<<<<<<
* cdef char * _filename
* # pointer to fastafile
*/
-struct __pyx_obj_5pysam_9csamtools_Fastafile {
+struct __pyx_obj_9csamtools_Fastafile {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtab;
+ struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
char *_filename;
faidx_t *fastafile;
};
-/* "pysam/csamtools.pxd":467
- * pass
+/* "csamtools.pxd":492
+ * cdef IteratorRowRegion rowiter
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam_iter_t iter # iterator state object
- * cdef bam1_t * b
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef int current_pos
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
+struct __pyx_obj_9csamtools_IteratorRowSelection {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtab;
bam1_t *b;
- int retval;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ int current_pos;
samfile_t *fp;
+ PyObject *positions;
int owns_samfile;
};
-/* "pysam/csamtools.pxd":504
+/* "csamtools.pxd":504
* cdef int cnext(self)
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
*
* # result of the last plbuf_push
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorColumn {
+struct __pyx_obj_9csamtools_IteratorColumn {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtab;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *iter;
+ struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *iter;
int tid;
int pos;
int n_plp;
int mask;
const bam_pileup1_t * plp;
bam_plp_t pileup_iter;
- __pyx_t_5pysam_9csamtools___iterdata iterdata;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
- struct __pyx_obj_5pysam_9csamtools_Fastafile *fastafile;
+ __pyx_t_9csamtools___iterdata iterdata;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ struct __pyx_obj_9csamtools_Fastafile *fastafile;
PyObject *stepper;
int max_depth;
};
-/* "pysam/csamtools.pxd":531
- * cdef reset( self, tid, start, end )
+/* "csamtools.pxd":536
+ * cdef int truncate
+ *
+ * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * cdef int start
- * cdef int end
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn __pyx_base;
- int start;
- int end;
- int truncate;
+struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
};
-/* "pysam/csamtools.pxd":480
- * cdef int cnext(self)
+/* "csamtools.pxd":467
+ * pass
*
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef samfile_t * fp
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam_iter_t iter # iterator state object
+ * cdef bam1_t * b
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowAll {
- struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtab;
+struct __pyx_obj_9csamtools_IteratorRowRegion {
+ struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
+ bam_iter_t iter;
bam1_t *b;
+ int retval;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
samfile_t *fp;
int owns_samfile;
};
-/* "pysam/csamtools.pxd":539
- * pass
+/* "csamtools.pyx":142
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
*
- * cdef class IndexedReads: # <<<<<<<<<<<<<<
- * cdef Samfile samfile
- * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_IndexedReads {
+struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr {
+ struct __pyx_Generator_object __pyx_base;
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "csamtools.pxd":420
+ * cdef bam1_t * _delegate
+ *
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to samfile
+ */
+struct __pyx_obj_9csamtools_Samfile {
PyObject_HEAD
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
- samfile_t *fp;
- PyObject *index;
- int owns_samfile;
+ struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
+ char *_filename;
+ samfile_t *samfile;
+ bam_index_t *index;
+ int isbam;
+ int isstream;
+ int isremote;
+ bam1_t *b;
+ char *mode;
+ int64_t start_offset;
};
-/* "pysam/csamtools.pyx":3222
+/* "csamtools.pyx":3222
* return retval, out_stderr, out_stdout
*
* cdef class SNPCall: # <<<<<<<<<<<<<<
* '''the results of a SNP call.'''
* cdef int _tid
*/
-struct __pyx_obj_5pysam_9csamtools_SNPCall {
+struct __pyx_obj_9csamtools_SNPCall {
PyObject_HEAD
int _tid;
int _pos;
@@ -631,62 +652,47 @@ struct __pyx_obj_5pysam_9csamtools_SNPCall {
};
-/* "pysam/csamtools.pyx":140
- * cdef char* CODE2CIGAR= "MIDNSHP=X"
- * if IS_PYTHON3:
- * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
- * else:
- * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
- */
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr {
- PyObject_HEAD
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
-};
-
-
-/* "pysam/csamtools.pxd":415
- * cdef char * _fetch( self, char * reference, int start, int end, int * length )
- *
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+/* "csamtools.pxd":539
+ * pass
*
- * # object that this AlignedRead represents
+ * cdef class IndexedReads: # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_AlignedRead {
+struct __pyx_obj_9csamtools_IndexedReads {
PyObject_HEAD
- bam1_t *_delegate;
+ struct __pyx_obj_9csamtools_Samfile *samfile;
+ samfile_t *fp;
+ PyObject *index;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":449
- * cdef char * _getrname( self, int tid )
+/* "csamtools.pxd":531
+ * cdef reset( self, tid, start, end )
*
- * cdef class PileupProxy: # <<<<<<<<<<<<<<
- * cdef bam_pileup1_t ** plp
- * cdef int tid
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * cdef int start
+ * cdef int end
*/
-struct __pyx_obj_5pysam_9csamtools_PileupProxy {
- PyObject_HEAD
- bam_pileup1_t **plp;
- int tid;
- int pos;
- int n_pu;
+struct __pyx_obj_9csamtools_IteratorColumnRegion {
+ struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+ int start;
+ int end;
+ int truncate;
};
-/* "pysam/csamtools.pxd":455
+/* "csamtools.pxd":455
* cdef int n_pu
*
* cdef class PileupRead: # <<<<<<<<<<<<<<
* cdef AlignedRead _alignment
* cdef int32_t _qpos
*/
-struct __pyx_obj_5pysam_9csamtools_PileupRead {
+struct __pyx_obj_9csamtools_PileupRead {
PyObject_HEAD
- struct __pyx_obj_5pysam_9csamtools_AlignedRead *_alignment;
+ struct __pyx_obj_9csamtools_AlignedRead *_alignment;
int32_t _qpos;
int _indel;
int _level;
@@ -696,20 +702,8 @@ struct __pyx_obj_5pysam_9csamtools_PileupRead {
};
-/* "pysam/csamtools.pxd":536
- * cdef int truncate
- *
- * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn __pyx_base;
-};
-
-
-/* "pysam/csamtools.pyx":1766
+/* "csamtools.pyx":1766
* return ret
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
@@ -717,61 +711,61 @@ struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs {
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn {
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *);
- char *(*getSequence)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *);
- PyObject *(*setMask)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *);
- PyObject *(*setupIteratorData)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args);
- PyObject *(*reset)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *);
+struct __pyx_vtabstruct_9csamtools_IteratorColumn {
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorColumn *);
+ char *(*getSequence)(struct __pyx_obj_9csamtools_IteratorColumn *);
+ PyObject *(*setMask)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *);
+ PyObject *(*setupIteratorData)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args);
+ PyObject *(*reset)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;
-/* "pysam/csamtools.pyx":1540
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
+/* "csamtools.pyx":1931
+ * self.iterdata.seq = NULL
*
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * '''iterates over a region only.
+ * '''
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
+struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion {
+ struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;
-/* "pysam/csamtools.pyx":375
- * ## Public methods
- * ######################################################################
- * cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
+/* "csamtools.pyx":1461
+ *
+ *
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
- char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
+struct __pyx_vtabstruct_9csamtools_IteratorRowRegion {
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowRegion *);
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowRegion *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion;
-/* "pysam/csamtools.pyx":1461
- *
+/* "csamtools.pyx":1641
+ * raise StopIteration
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile)*
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
+struct __pyx_vtabstruct_9csamtools_IteratorRowSelection {
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection;
-/* "pysam/csamtools.pyx":1968
+/* "csamtools.pyx":1968
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
@@ -779,60 +773,62 @@ static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtabpt
* """
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs {
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
-/* "pysam/csamtools.pyx":1641
- * raise StopIteration
+/* "csamtools.pyx":545
*
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile)*
*
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
+ * add_sq_text = False, check_header = True, check_sq = True )*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
+struct __pyx_vtabstruct_9csamtools_Samfile {
+ bam_header_t *(*_buildHeader)(struct __pyx_obj_9csamtools_Samfile *, PyObject *);
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_Samfile *);
+ int (*cnext)(struct __pyx_obj_9csamtools_Samfile *);
+ int (*write)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch);
+ char *(*_getrname)(struct __pyx_obj_9csamtools_Samfile *, int);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile;
-/* "pysam/csamtools.pyx":1931
- * self.iterdata.seq = NULL
+/* "csamtools.pyx":375
+ * ## Public methods
+ * ######################################################################
+ * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * '''iterates over a region only.
- * '''
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion {
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_vtabstruct_9csamtools_Fastafile {
+ char *(*_fetch)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile;
-/* "pysam/csamtools.pyx":545
+/* "csamtools.pyx":1540
+ * if self.owns_samfile: samclose( self.fp )
*
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int reopen = True)*
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
- * add_sq_text = False, check_header = True, check_sq = True )*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_Samfile {
- bam_header_t *(*_buildHeader)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *);
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_Samfile *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_Samfile *);
- int (*write)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch);
- char *(*_getrname)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int);
+struct __pyx_vtabstruct_9csamtools_IteratorRowAll {
+ bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowAll *);
+ int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
+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);
@@ -845,21 +841,8 @@ static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9
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__)
@@ -870,7 +853,7 @@ static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9
#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)
@@ -881,21 +864,23 @@ static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9
#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
@@ -903,14 +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(); \
@@ -920,25 +908,25 @@ 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 PyObject* __Pyx_decode_c_string(
- const char* cstring, Py_ssize_t start, Py_ssize_t stop,
- const char* encoding, const char* errors,
- PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
+#endif /* CYTHON_PROFILE */
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -954,13 +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*/
@@ -970,6 +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;
@@ -977,107 +966,79 @@ 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 CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
+
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
- __Pyx_GetItemInt_Fast(o, i) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i)))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (PyList_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, n);
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
Py_INCREF(r);
return r;
}
- }
- else if (PyTuple_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);
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
Py_INCREF(r);
return r;
}
- } else { /* inlined PySequence_GetItem() */
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return NULL;
- i += l;
- }
- return m->sq_item(o, i);
- }
}
-#else
- if (PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len)) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
+
+#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
+ __Pyx_GetItemInt_Fast(o, i) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+ PyObject *r;
+ if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
}
- return PyList_Append(list, x);
+ else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
+ r = PySequence_GetItem(o, i);
+ }
+ else {
+ r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ }
+ return r;
}
-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (unlikely(PyList_Append(L, x) < 0)) return NULL;
+ if (PyList_Append(L, x) < 0) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- } else {
+ }
+ else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
@@ -1087,27 +1048,28 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
}
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
+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_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
- int result = PySequence_Contains(seq, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+ return unlikely(b < 0) ? b : !b;
}
-
-static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
- int result = PyDict_Contains(dict, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
+ return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
}
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
+ if (unlikely(d == Py_None)) {
+ __Pyx_RaiseNoneIndexingError();
+ return NULL;
+ }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -1133,6 +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;
@@ -1143,7 +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
@@ -1159,6 +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;
@@ -1166,29 +1130,16 @@ 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 CYTHON_COMPILING_IN_PYPY
- if (PySequence_Check(o)) {
+ 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);
}
-#else
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return -1;
- i += l;
- }
- return m->sq_ass_item(o, i, (PyObject *)NULL);
- }
-#endif
- return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i));
}
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
@@ -1199,51 +1150,29 @@ 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 <structmember.h>
-#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 CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
+static PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
+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*/
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t);
@@ -1257,8 +1186,12 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
+
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t);
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
+
static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject *);
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
@@ -1299,33 +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 <structmember.h>
-#include <frameobject.h>
-typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
-typedef struct {
- PyObject_HEAD
- __pyx_generator_body_t body;
- PyObject *closure;
- PyObject *exc_type;
- PyObject *exc_value;
- PyObject *exc_traceback;
- PyObject *gi_weakreflist;
- PyObject *classobj;
- PyObject *yieldfrom;
- int resume_label;
- char is_running; // using T_BOOL for property below requires char value
-} __pyx_GeneratorObject;
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure);
-static int __pyx_Generator_init(void);
-static int __Pyx_Generator_clear(PyObject* self);
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
-#else
-#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
-#endif
-
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename); /*proto*/
@@ -1333,38 +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 PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-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 PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-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' */
@@ -1389,10 +1272,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'cpython.iterator' */
-/* Module declarations from '__builtin__' */
-
/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
/* Module declarations from 'cpython.number' */
@@ -1446,53 +1326,54 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from 'cpython' */
-/* Module declarations from 'pysam.csamtools' */
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastafile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_AlignedRead = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Samfile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupProxy = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupRead = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRow = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowRegion = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAll = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowSelection = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumn = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IndexedReads = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools_SNPCall = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = 0;
-static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = 0;
-static PyObject *__pyx_v_5pysam_9csamtools__FILENAME_ENCODING = 0;
-static char *__pyx_v_5pysam_9csamtools_CODE2CIGAR;
-static char *__pyx_v_5pysam_9csamtools_bam_nt16_rev_table;
-static int __pyx_v_5pysam_9csamtools_max_pos;
-static PyObject *__pyx_f_5pysam_9csamtools_from_string_and_size(char *, size_t); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__my_encodeFilename(PyObject *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__force_bytes(PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__charptr_to_str(char *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools__force_str(PyObject *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
-static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_count_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_5pysam_9csamtools___advance_all(void *, bam1_t *); /*proto*/
-static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-#define __Pyx_MODULE_NAME "pysam.csamtools"
-int __pyx_module_is_main_pysam__csamtools = 0;
-
-/* Implementation of 'pysam.csamtools' */
+/* Module declarations from 'csamtools' */
+static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
+static PyTypeObject *__pyx_ptype_9csamtools_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;
+static char *__pyx_v_9csamtools_CODE2CIGAR;
+static char *__pyx_v_9csamtools_bam_nt16_rev_table;
+static int __pyx_v_9csamtools_max_pos;
+static PyObject *__pyx_f_9csamtools_from_string_and_size(char *, size_t); /*proto*/
+static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools__charptr_to_str(char *); /*proto*/
+static PyObject *__pyx_f_9csamtools__force_str(PyObject *); /*proto*/
+static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
+static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/
+static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
+static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/
+static int __pyx_f_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_count_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_9csamtools___advance_all(void *, bam1_t *); /*proto*/
+static int __pyx_f_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *); /*proto*/
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
+#define __Pyx_MODULE_NAME "csamtools"
+int __pyx_module_is_main_csamtools = 0;
+
+/* Implementation of 'csamtools' */
static PyObject *__pyx_builtin_object;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_enumerate;
@@ -1513,191 +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_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static Py_ssize_t __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_6_open(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_5pysam_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_5pysam_9csamtools_7Samfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_5pysam_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_5pysam_9csamtools_7Samfile_8gettid(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_5pysam_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_5pysam_9csamtools_7Samfile_14reset(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_16seek(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_18tell(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_20fetch(struct __pyx_obj_5pysam_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_5pysam_9csamtools_7Samfile_22mate(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5pysam_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_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5pysam_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_5pysam_9csamtools_7Samfile_28close(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_32write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(struct __pyx_obj_5pysam_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_5pysam_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_42__next__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_5pysam_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_5pysam_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_5pysam_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_5pysam_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_other); /* proto */
-static Py_hash_t __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_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_5pysam_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall___str__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_2build(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_4find(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static void __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_5pysam_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";
@@ -1755,7 +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";
@@ -1887,12 +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[] = "pysam.csamtools";
-static char __pyx_k_258[] = "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_267[] = "\n stderr is captured.\n ";
-static char __pyx_k_274[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_291[] = "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";
@@ -1935,11 +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";
@@ -1984,7 +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";
@@ -2022,7 +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";
@@ -2072,10 +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";
@@ -2085,6 +1770,7 @@ static char __pyx_k__TypeError[] = "TypeError";
static char __pyx_k____enter__[] = "__enter__";
static char __pyx_k___hasIndex[] = "_hasIndex";
static char __pyx_k__alignment[] = "alignment";
+static char __pyx_k__csamtools[] = "csamtools";
static char __pyx_k__enumerate[] = "enumerate";
static char __pyx_k__exc_value[] = "exc_value";
static char __pyx_k__fastafile[] = "fastafile";
@@ -2102,8 +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";
@@ -2116,7 +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";
@@ -2209,13 +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_n_s_257;
-static PyObject *__pyx_kp_s_258;
-static PyObject *__pyx_kp_s_267;
-static PyObject *__pyx_kp_s_274;
+static PyObject *__pyx_kp_s_262;
static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_291;
static PyObject *__pyx_kp_u_3;
static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_kp_s_31;
@@ -2344,7 +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;
@@ -2357,7 +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;
@@ -2368,6 +2047,7 @@ static PyObject *__pyx_n_s__collections;
static PyObject *__pyx_n_s__compile;
static PyObject *__pyx_n_s__consensus_quality;
static PyObject *__pyx_n_s__coverage;
+static PyObject *__pyx_n_s__csamtools;
static PyObject *__pyx_n_s__ctypes;
static PyObject *__pyx_n_s__d;
static PyObject *__pyx_n_s__data_len;
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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;
@@ -2434,13 +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;
@@ -2473,7 +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;
@@ -2491,12 +2166,7 @@ static PyObject *__pyx_n_s__split;
static PyObject *__pyx_n_s__start;
static PyObject *__pyx_n_s__startswith;
static PyObject *__pyx_n_s__stderr;
-static PyObject *__pyx_n_s__stderr_f;
-static PyObject *__pyx_n_s__stderr_h;
static PyObject *__pyx_n_s__stdout;
-static PyObject *__pyx_n_s__stdout_f;
-static PyObject *__pyx_n_s__stdout_h;
-static PyObject *__pyx_n_s__stdout_save;
static PyObject *__pyx_n_s__stepper;
static PyObject *__pyx_n_s__streams;
static PyObject *__pyx_n_s__strip;
@@ -2629,43 +2299,14 @@ static PyObject *__pyx_k_tuple_182;
static PyObject *__pyx_k_tuple_183;
static PyObject *__pyx_k_tuple_184;
static PyObject *__pyx_k_tuple_252;
-static PyObject *__pyx_k_tuple_254;
+static PyObject *__pyx_k_tuple_257;
+static PyObject *__pyx_k_tuple_258;
static PyObject *__pyx_k_tuple_259;
+static PyObject *__pyx_k_tuple_260;
static PyObject *__pyx_k_tuple_261;
-static PyObject *__pyx_k_tuple_263;
-static PyObject *__pyx_k_tuple_265;
-static PyObject *__pyx_k_tuple_268;
-static PyObject *__pyx_k_tuple_270;
-static PyObject *__pyx_k_tuple_272;
-static PyObject *__pyx_k_tuple_275;
-static PyObject *__pyx_k_tuple_276;
-static PyObject *__pyx_k_tuple_277;
-static PyObject *__pyx_k_tuple_278;
-static PyObject *__pyx_k_tuple_279;
-static PyObject *__pyx_k_tuple_280;
-static PyObject *__pyx_k_tuple_282;
-static PyObject *__pyx_k_tuple_283;
-static PyObject *__pyx_k_tuple_285;
-static PyObject *__pyx_k_tuple_287;
-static PyObject *__pyx_k_tuple_289;
-static PyObject *__pyx_k_tuple_292;
-static PyObject *__pyx_k_codeobj_255;
-static PyObject *__pyx_k_codeobj_260;
-static PyObject *__pyx_k_codeobj_262;
-static PyObject *__pyx_k_codeobj_264;
-static PyObject *__pyx_k_codeobj_266;
-static PyObject *__pyx_k_codeobj_269;
-static PyObject *__pyx_k_codeobj_271;
-static PyObject *__pyx_k_codeobj_273;
-static PyObject *__pyx_k_codeobj_281;
-static PyObject *__pyx_k_codeobj_284;
-static PyObject *__pyx_k_codeobj_286;
-static PyObject *__pyx_k_codeobj_288;
-static PyObject *__pyx_k_codeobj_290;
-static PyObject *__pyx_k_codeobj_293;
-static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
-
-/* "pysam/csamtools.pyx":140
+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"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
@@ -2673,35 +2314,29 @@ static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope;
+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;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
__Pyx_TraceDeclarations
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- __pyx_cur_scope = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr->tp_new(__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr, __pyx_empty_tuple, NULL);
+ __Pyx_RefNannySetupContext("genexpr");
+ __pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct__genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct__genexpr, __pyx_empty_tuple, NULL);
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__Pyx_RefNannyFinishContext();
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__Pyx_GOTREF(__pyx_cur_scope);
__Pyx_TraceCall("genexpr", __pyx_f[0], 140);
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- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_4generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_cur_scope);
- __Pyx_RefNannyFinishContext();
- return (PyObject *) gen;
- }
+ __pyx_self = __pyx_self;
+ __pyx_cur_scope->__pyx_base.resume_label = 0;
+ __pyx_cur_scope->__pyx_base.body = (__pyx_generator_body_t) __pyx_gb_9csamtools_2generator;
+ __Pyx_GIVEREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) __pyx_cur_scope;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
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@@ -2709,17 +2344,16 @@ static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__p
return __pyx_r;
}
-static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value) /* generator body */
{
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *(*__pyx_t_4)(PyObject *);
__Pyx_RefNannyDeclarations
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@@ -2730,7 +2364,7 @@ static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__
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*/
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- struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_dest = 0;
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__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
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const char *__pyx_filename = NULL;
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* cdef class PileupProxy
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- __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_t_1);
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* cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ):
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*/
__pyx_v_dest->plp = __pyx_v_plp;
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*/
__pyx_v_dest->tid = __pyx_v_tid;
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*/
__pyx_v_dest->pos = __pyx_v_pos;
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goto __pyx_L0;
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__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("pysam.csamtools.makePileupProxy", __pyx_clineno, __pyx_lineno, __pyx_filename);
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return __pyx_r;
}
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* cdef class PileupRead
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-static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
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+static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
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const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
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* cdef makePileupRead( bam_pileup1_t * src ):
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__pyx_t_1 = 0;
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__pyx_t_1 = 0;
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* dest._level = src.level
*/
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* dest._is_del = src.is_del
*/
- __pyx_t_3 = __pyx_v_src->indel;
- __pyx_v_dest->_indel = __pyx_t_3;
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* dest._is_head = src.is_head
*/
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*/
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*/
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__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
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return __pyx_r;
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-static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
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char __pyx_v_auxtype;
uint8_t __pyx_v_byte_size;
int32_t __pyx_v_nvalues;
PyObject *__pyx_v_values = NULL;
- CYTHON_UNUSED long __pyx_v_x;
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*/
__pyx_v_auxtype = (__pyx_v_s[0]);
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__pyx_v_byte_size = bam_aux_type2size(__pyx_v_auxtype);
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__pyx_v_nvalues = (((int32_t *)__pyx_v_s)[0]);
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__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_v_start);
__pyx_v_start = __pyx_int_0;
- goto __pyx_L6;
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__pyx_t_3 = (__pyx_v_end == Py_None);
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__Pyx_DECREF(__pyx_v_end);
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- __pyx_L7:;
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+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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__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);
@@ -5947,7 +5432,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
__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;
@@ -5957,18 +5442,19 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
__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:;
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+ /* "csamtools.pyx":467
*
* if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
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+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
@@ -5976,23 +5462,25 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
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__pyx_r = ((PyObject *)__pyx_kp_b_16);
goto __pyx_L0;
- goto __pyx_L9;
+ goto __pyx_L12;
}
- __pyx_L9:;
+ __pyx_L12:;
- /* "pysam/csamtools.pyx":469
+ /* "csamtools.pyx":469
* if start == end: return b""
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* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
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* # note: faidx_fetch_seq has a bug such that out-of-range access
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- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_5pysam_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); 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_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -6002,7 +5490,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
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__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;
@@ -6012,23 +5500,25 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
__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:;
- /* "pysam/csamtools.pyx":470
+ /* "csamtools.pyx":470
* # valid ranges are from 0 to 2^29-1
* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
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- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_5pysam_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -6038,7 +5528,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
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__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;
@@ -6048,11 +5538,11 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
__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:;
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+ /* "csamtools.pyx":479
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__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);
@@ -6079,7 +5569,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
__pyx_v_region = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":480
+ /* "csamtools.pyx":480
* # &length)
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@@ -6089,7 +5579,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_
__pyx_t_3 = (PY_MAJOR_VERSION >= 3);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":481
+ /* "csamtools.pyx":481
* region = "%s:%i-%i" % (reference, start+1, end)
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__Pyx_DECREF(__pyx_v_region);
__pyx_v_region = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L12;
+ goto __pyx_L15;
}
- __pyx_L12:;
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- /* "pysam/csamtools.pyx":484
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- __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*/ {
- /* "pysam/csamtools.pyx":487
+ /* "csamtools.pyx":487
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- __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
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}
- __pyx_L4:;
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}
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*
*/
- __pyx_t_1 = (__pyx_v_self->samfile != NULL);
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*/
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__pyx_v_header_to_write = NULL;
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+ __pyx_t_8 = ((PyObject *)__pyx_f_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_bmode = ((PyObject*)__pyx_t_5);
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ goto __pyx_L8_unpacking_done;
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__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
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- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L5_unpacking_done:;
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__pyx_v_rend = __pyx_t_13;
- /* "pysam/csamtools.pyx":929
+ /* "csamtools.pyx":929
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*
* if self.isstream: reopen = False # <<<<<<<<<<<<<<
* 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*/ {
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+ /* "csamtools.pyx":930
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*/
__pyx_v_reopen = 1;
}
- __pyx_L6:;
+ __pyx_L9:;
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+ /* "csamtools.pyx":932
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* if not until_eof and not self._hasIndex() and not self.isremote:
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*/
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__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);
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}
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+ /* "csamtools.pyx":934
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
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if (__pyx_t_14) {
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
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PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
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+ /* "csamtools.pyx":994
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*/
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Py_ssize_t index = -1;
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- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
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+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_rstart = __pyx_t_11;
__pyx_v_rend = __pyx_t_12;
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*/
__pyx_v_counter = 0;
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*/
- if (__pyx_v_self->isbam) {
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if (__pyx_t_3) {
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+ __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;}
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__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_13 = (!__pyx_t_4);
if (__pyx_t_13) {
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@@ -11372,7 +10652,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
}
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_5 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L9;
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/*else*/ {
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- __pyx_L6:;
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+ PyObject *(*__pyx_t_9)(PyObject *);
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+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
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__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
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__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_12 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_data = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1366
+ /* "csamtools.pyx":1366
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+ __pyx_t_5 = ((PySequence_Contains(__pyx_t_6, __pyx_v_record))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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if (__pyx_t_5) {
- /* "pysam/csamtools.pyx":1368
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* for fields in new_header[record]:
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+ 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;}
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__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;}
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- __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);
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}
/*else*/ {
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+ /* "csamtools.pyx":1370
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__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;
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- #endif
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) {
+ __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
- __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- #endif
+ __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
} else {
__pyx_t_11 = __pyx_t_10(__pyx_t_1);
if (unlikely(!__pyx_t_11)) {
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__pyx_v_fields = __pyx_t_11;
__pyx_t_11 = 0;
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* 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;}
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__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;}
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- __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);
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- /* "pysam/csamtools.pyx":1373
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__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));
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__pyx_v_text = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":1374
+ /* "csamtools.pyx":1374
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}
__pyx_L18:;
- /* "pysam/csamtools.pyx":1375
+ /* "csamtools.pyx":1375
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__pyx_v_dest->text = ((char *)calloc(__pyx_t_3, (sizeof(char))));
- /* "pysam/csamtools.pyx":1376
+ /* "csamtools.pyx":1376
* if dest.text != NULL: free( dest.text )
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__pyx_v_dest->l_text = __pyx_t_3;
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__pyx_t_7 = 0;
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strncpy(__pyx_v_dest->text, __pyx_t_13, __pyx_v_dest->l_text);
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+ __pyx_t_5 = ((PySequence_Contains(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
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- __Pyx_GOTREF(__pyx_t_7);
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__pyx_v_seqs = __pyx_t_7;
__pyx_t_7 = 0;
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__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
- if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
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- #endif
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- #endif
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__pyx_t_7 = __pyx_t_4(__pyx_t_1);
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__pyx_t_7 = 0;
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__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;}
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int __pyx_clineno = 0;
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*/
- __pyx_v_ret = samread(__pyx_v_self->samfile, __pyx_v_self->b);
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- /* "pysam/csamtools.pyx":1433
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+ __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;}
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- struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
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+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) {
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int __pyx_v_tid;
int __pyx_v_beg;
int __pyx_v_end;
int __pyx_v_reopen;
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+ char *__pyx_t_5;
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else goto __pyx_L5_argtuple_error;
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else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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default: goto __pyx_L5_argtuple_error;
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}
- __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
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__pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__pyx_L3_error:;
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__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1703);
- /* "pysam/csamtools.pyx":1704
+ /* "csamtools.pyx":1704
*
* def __dealloc__(self):
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b);
- /* "pysam/csamtools.pyx":1705
+ /* "csamtools.pyx":1705
* def __dealloc__(self):
* bam_destroy1(self.b)
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* ##-------------------------------------------------------------------
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
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-/* "pysam/csamtools.pyx":1710
+/* "csamtools.pyx":1710
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef int __advance_all( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
@@ -18306,24 +17155,24 @@ static void __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(struc
* '''
*/
-static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_5pysam_9csamtools___iterdata *__pyx_v_d;
+static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_9csamtools___iterdata *__pyx_v_d;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_all", 0);
+ __Pyx_RefNannySetupContext("__advance_all");
__Pyx_TraceCall("__advance_all", __pyx_f[0], 1710);
- /* "pysam/csamtools.pyx":1714
+ /* "csamtools.pyx":1714
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
* return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
*/
- __pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
+ __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
- /* "pysam/csamtools.pyx":1715
+ /* "csamtools.pyx":1715
* cdef __iterdata * d
* d = <__iterdata*>data
* return bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
@@ -18340,7 +17189,7 @@ static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *_
return __pyx_r;
}
-/* "pysam/csamtools.pyx":1717
+/* "csamtools.pyx":1717
* return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* cdef int __advance_snpcalls( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
@@ -18348,8 +17197,8 @@ static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *_
* the samtools pileup.
*/
-static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_5pysam_9csamtools___iterdata *__pyx_v_d;
+static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_9csamtools___iterdata *__pyx_v_d;
int __pyx_v_ret;
int __pyx_v_skip;
int __pyx_v_q;
@@ -18361,28 +17210,27 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
- int32_t __pyx_t_4;
+ PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- long __pyx_t_8;
+ long __pyx_t_7;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_snpcalls", 0);
+ __Pyx_RefNannySetupContext("__advance_snpcalls");
__Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1717);
- /* "pysam/csamtools.pyx":1722
+ /* "csamtools.pyx":1722
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*/
- __pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
+ __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
- /* "pysam/csamtools.pyx":1724
+ /* "csamtools.pyx":1724
* d = <__iterdata*>data
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
@@ -18391,7 +17239,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
- /* "pysam/csamtools.pyx":1725
+ /* "csamtools.pyx":1725
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
* cdef int skip = 0 # <<<<<<<<<<<<<<
@@ -18400,7 +17248,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_skip = 0;
- /* "pysam/csamtools.pyx":1727
+ /* "csamtools.pyx":1727
* cdef int skip = 0
* cdef int q
* cdef int is_cns = 1 # <<<<<<<<<<<<<<
@@ -18409,7 +17257,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_is_cns = 1;
- /* "pysam/csamtools.pyx":1728
+ /* "csamtools.pyx":1728
* cdef int q
* cdef int is_cns = 1
* cdef int is_nobaq = 0 # <<<<<<<<<<<<<<
@@ -18418,7 +17266,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_is_nobaq = 0;
- /* "pysam/csamtools.pyx":1729
+ /* "csamtools.pyx":1729
* cdef int is_cns = 1
* cdef int is_nobaq = 0
* cdef int capQ_thres = 0 # <<<<<<<<<<<<<<
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*/
__pyx_v_capQ_thres = 0;
- /* "pysam/csamtools.pyx":1732
+ /* "csamtools.pyx":1732
*
* # reload sequence
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@@ -18443,7 +17291,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1733
+ /* "csamtools.pyx":1733
* # reload sequence
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@@ -18457,26 +17305,25 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L4:;
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+ /* "csamtools.pyx":1734
* if d.fastafile != NULL and b.core.tid != d.tid:
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* d.tid = b.core.tid # <<<<<<<<<<<<<<
* d.seq = faidx_fetch_seq(d.fastafile,
* d.samfile.header.target_name[d.tid],
*/
- __pyx_t_4 = __pyx_v_b->core.tid;
- __pyx_v_d->tid = __pyx_t_4;
+ __pyx_v_d->tid = __pyx_v_b->core.tid;
- /* "pysam/csamtools.pyx":1735
+ /* "csamtools.pyx":1735
* if d.seq != NULL: free(d.seq)
* d.tid = b.core.tid
* d.seq = faidx_fetch_seq(d.fastafile, # <<<<<<<<<<<<<<
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*/
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+ __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_9csamtools_max_pos, (&__pyx_v_d->seq_len));
- /* "pysam/csamtools.pyx":1739
+ /* "csamtools.pyx":1739
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@@ -18486,46 +17333,46 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__pyx_t_3 = (__pyx_v_d->seq == NULL);
if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":1741
+ /* "csamtools.pyx":1741
* if d.seq == NULL:
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*/
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- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_4 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- /* "pysam/csamtools.pyx":1742
+ /* "csamtools.pyx":1742
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
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*
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- __pyx_t_6 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __Pyx_GIVEREF(__pyx_t_6);
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- __Pyx_Raise(__pyx_t_6, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
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+ __Pyx_GOTREF(__pyx_t_5);
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
}
@@ -18534,7 +17381,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1745
+ /* "csamtools.pyx":1745
*
*
* while ret >= 0: # <<<<<<<<<<<<<<
@@ -18545,7 +17392,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__pyx_t_3 = (__pyx_v_ret >= 0);
if (!__pyx_t_3) break;
- /* "pysam/csamtools.pyx":1747
+ /* "csamtools.pyx":1747
* while ret >= 0:
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@@ -18554,7 +17401,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_skip = 0;
- /* "pysam/csamtools.pyx":1750
+ /* "csamtools.pyx":1750
*
* # realign read - changes base qualities
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@@ -18579,7 +17426,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L8:;
- /* "pysam/csamtools.pyx":1752
+ /* "csamtools.pyx":1752
* if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq )
*
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@@ -18595,7 +17442,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":1753
+ /* "csamtools.pyx":1753
*
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres) # <<<<<<<<<<<<<<
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*/
__pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
- /* "pysam/csamtools.pyx":1754
+ /* "csamtools.pyx":1754
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1 # <<<<<<<<<<<<<<
@@ -18617,7 +17464,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
goto __pyx_L10;
}
- /* "pysam/csamtools.pyx":1755
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* q = bam_cap_mapQ(b, d.seq, capQ_thres)
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}
__pyx_L9:;
- /* "pysam/csamtools.pyx":1756
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* if q < 0: skip = 1
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*
*/
- __pyx_t_8 = (__pyx_v_b->core.flag & 4);
- if (__pyx_t_8) {
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__pyx_v_skip = 1;
goto __pyx_L11;
}
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* elif b.core.qual > q: b.core.qual = q
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* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1 # <<<<<<<<<<<<<<
@@ -18666,7 +17513,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L11:;
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* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
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}
__pyx_L12:;
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}
__pyx_L7_break:;
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__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
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__Pyx_XDECREF(__pyx_t_5);
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@@ -18715,85 +17562,70 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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goto __pyx_L3;
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- /* "pysam/csamtools.pyx":1887
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goto __pyx_L4;
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PyObject *__pyx_t_3 = NULL;
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int __pyx_lineno = 0;
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*/
__pyx_t_5.__pyx_n = 1;
__pyx_t_5.reopen = 0;
- __pyx_t_4 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_5pysam_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = ((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_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2002; __pyx_clineno = __LINE_ [...]
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L7;
+ goto __pyx_L9;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2004
+ /* "csamtools.pyx":2004
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* else:
* raise StopIteration # <<<<<<<<<<<<<<
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__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L7:;
+ __pyx_L9:;
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__pyx_r = Py_None; __Pyx_INCREF(Py_None);
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__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("pysam.csamtools.IteratorColumnAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":2009
+/* "csamtools.pyx":2009
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef inline int32_t query_start(bam1_t *src) except -1: # <<<<<<<<<<<<<<
@@ -20481,7 +19220,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
* cdef uint32_t k
*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx_v_src) {
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) {
uint32_t *__pyx_v_cigar_p;
uint32_t __pyx_v_op;
uint32_t __pyx_v_k;
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int __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
__Pyx_TraceDeclarations
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- /* "pysam/csamtools.pyx":2012
+ /* "csamtools.pyx":2012
* cdef uint32_t * cigar_p, op
* cdef uint32_t k
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*/
__pyx_v_start_offset = 0;
- /* "pysam/csamtools.pyx":2014
+ /* "csamtools.pyx":2014
* cdef uint32_t start_offset = 0
*
* if src.core.n_cigar: # <<<<<<<<<<<<<<
@@ -20515,7 +19254,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
*/
if (__pyx_v_src->core.n_cigar) {
- /* "pysam/csamtools.pyx":2015
+ /* "csamtools.pyx":2015
*
* if src.core.n_cigar:
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
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*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2016
+ /* "csamtools.pyx":2016
* if src.core.n_cigar:
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
@@ -20534,7 +19273,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
__pyx_t_1 = __pyx_v_src->core.n_cigar;
for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2017
+ /* "csamtools.pyx":2017
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
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*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2022
+ /* "csamtools.pyx":2022
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
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*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2018
+ /* "csamtools.pyx":2018
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
@@ -20561,7 +19300,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
*/
case 5:
- /* "pysam/csamtools.pyx":2019
+ /* "csamtools.pyx":2019
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
@@ -20577,7 +19316,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2020
+ /* "csamtools.pyx":2020
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
@@ -20589,7 +19328,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
PyErr_SetString(__pyx_t_5, __pyx_k_132);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/csamtools.pyx":2021
+ /* "csamtools.pyx":2021
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
@@ -20603,7 +19342,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2022
+ /* "csamtools.pyx":2022
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -20612,7 +19351,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
*/
case 4:
- /* "pysam/csamtools.pyx":2023
+ /* "csamtools.pyx":2023
* return -1
* elif op==BAM_CSOFT_CLIP:
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
@@ -20623,7 +19362,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
break;
default:
- /* "pysam/csamtools.pyx":2025
+ /* "csamtools.pyx":2025
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
@@ -20639,7 +19378,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2027
+ /* "csamtools.pyx":2027
* break
*
* return start_offset # <<<<<<<<<<<<<<
@@ -20656,7 +19395,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2032
+/* "csamtools.pyx":2032
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<<
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* cdef uint32_t k
*/
-static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v_src) {
+static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
uint32_t *__pyx_v_cigar_p;
uint32_t __pyx_v_op;
uint32_t __pyx_v_k;
uint32_t __pyx_v_end_offset;
int32_t __pyx_r;
__Pyx_RefNannyDeclarations
- int32_t __pyx_t_1;
+ int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_4 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_end", 0);
+ __Pyx_RefNannySetupContext("query_end");
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- /* "pysam/csamtools.pyx":2035
+ /* "csamtools.pyx":2035
* cdef uint32_t * cigar_p, op
* cdef uint32_t k
* cdef uint32_t end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
*
* if src.core.n_cigar>1:
*/
- __pyx_t_1 = __pyx_v_src->core.l_qseq;
- __pyx_v_end_offset = __pyx_t_1;
+ __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
- /* "pysam/csamtools.pyx":2037
+ /* "csamtools.pyx":2037
* cdef uint32_t end_offset = src.core.l_qseq
*
* if src.core.n_cigar>1: # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1:
*/
- __pyx_t_2 = (__pyx_v_src->core.n_cigar > 1);
- if (__pyx_t_2) {
+ __pyx_t_1 = (__pyx_v_src->core.n_cigar > 1);
+ if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2038
+ /* "csamtools.pyx":2038
*
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
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*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2039
+ /* "csamtools.pyx":2039
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1: # <<<<<<<<<<<<<<
@@ -20718,7 +19455,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) {
- /* "pysam/csamtools.pyx":2040
+ /* "csamtools.pyx":2040
* cigar_p = bam1_cigar(src);
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*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2045
+ /* "csamtools.pyx":2045
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -20736,7 +19473,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2041
+ /* "csamtools.pyx":2041
* for k from src.core.n_cigar > k >= 1:
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@@ -20745,35 +19482,35 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
case 5:
- /* "pysam/csamtools.pyx":2042
+ /* "csamtools.pyx":2042
* op = cigar_p[k] & BAM_CIGAR_MASK
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*/
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- __pyx_t_3 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
- __pyx_t_4 = __pyx_t_3;
+ __pyx_t_1 = (__pyx_v_end_offset != 0);
+ if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
+ __pyx_t_3 = __pyx_t_2;
} else {
- __pyx_t_4 = __pyx_t_2;
+ __pyx_t_3 = __pyx_t_1;
}
- if (__pyx_t_4) {
+ if (__pyx_t_3) {
- /* "pysam/csamtools.pyx":2043
+ /* "csamtools.pyx":2043
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- PyErr_SetString(__pyx_t_5, __pyx_k_132);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_4 = __pyx_builtin_ValueError;
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+ PyErr_SetString(__pyx_t_4, __pyx_k_132);
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* return -1 # <<<<<<<<<<<<<<
@@ -20787,7 +19524,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2045
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*/
case 4:
- /* "pysam/csamtools.pyx":2046
+ /* "csamtools.pyx":2046
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break;
default:
- /* "pysam/csamtools.pyx":2048
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}
__pyx_L3:;
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*
*/
- __pyx_t_4 = (__pyx_v_end_offset == 0);
- if (__pyx_t_4) {
+ __pyx_t_3 = (__pyx_v_end_offset == 0);
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* return end_offset
*/
- __pyx_t_1 = __pyx_v_src->core.l_qseq;
- __pyx_v_end_offset = __pyx_t_1;
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goto __pyx_L7;
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__pyx_L7:;
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+static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
uint8_t *__pyx_v_p;
uint32_t __pyx_v_k;
char *__pyx_v_s;
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const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
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* cdef char * s
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__pyx_t_1 = (!__pyx_v_src->core.l_qseq);
if (__pyx_t_1) {
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}
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__pyx_v_seq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
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for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
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+ (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
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goto __pyx_L0;
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__pyx_t_1 = 0;
goto __pyx_L0;
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__pyx_t_1 = 0;
goto __pyx_L0;
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__pyx_t_1 = 0;
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__pyx_t_1 = 0;
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__pyx_t_4 = 0;
goto __pyx_L0;
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@@ -35322,7 +32807,7 @@ static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
};
static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*mp_length*/
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
@@ -35348,12 +32833,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_Fastafile = {
+static PyTypeObject __pyx_type_9csamtools_Fastafile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.Fastafile"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_Fastafile), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_Fastafile, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -35380,9 +32865,9 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Fastafile = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_Fastafile, /*tp_methods*/
+ __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_Fastafile, /*tp_getset*/
+ __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -35390,7 +32875,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Fastafile = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_Fastafile, /*tp_new*/
+ __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -35404,18 +32889,18 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Fastafile = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_AlignedRead(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_AlignedRead(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_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);
@@ -35423,13 +32908,13 @@ static void __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5qname___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35437,13 +32922,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35451,13 +32936,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35465,13 +32950,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3seq___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35479,13 +32964,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, PyObje
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4qual___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35493,33 +32978,33 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_query(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5query___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qqual(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qstart(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qend(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4qend___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qlen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4tags___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35527,13 +33012,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35541,13 +33026,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35555,13 +33040,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tid(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35569,13 +33054,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid(PyObject *o, PyObje
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_pos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35583,13 +33068,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pos(PyObject *o, PyObje
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35597,25 +33082,25 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, PyObje
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rlen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aend(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_alen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35623,13 +33108,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35637,13 +33122,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35651,13 +33136,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35665,13 +33150,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35679,13 +33164,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35693,13 +33178,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35707,13 +33192,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35721,13 +33206,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o,
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35735,13 +33220,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35749,13 +33234,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35763,13 +33248,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObje
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35777,13 +33262,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o,
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35791,13 +33276,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObjec
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35805,13 +33290,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, P
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35819,13 +33304,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, P
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35833,13 +33318,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35847,13 +33332,13 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o,
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_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__");
@@ -35861,62 +33346,62 @@ static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_positions(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_AlignedRead[] = {
- {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_7compare, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_6compare)},
- {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_11overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_10overlap)},
- {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_13opt, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_12opt)},
- {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_15fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_14fancy_str)},
+static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = {
+ {__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}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_AlignedRead[] = {
- {(char *)"qname", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qname, __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_188), 0},
- {(char *)"cigar", __pyx_getprop_5pysam_9csamtools_11AlignedRead_cigar, __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_189), 0},
- {(char *)"cigarstring", __pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_190), 0},
- {(char *)"seq", __pyx_getprop_5pysam_9csamtools_11AlignedRead_seq, __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_191), 0},
- {(char *)"qual", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qual, __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_192), 0},
- {(char *)"query", __pyx_getprop_5pysam_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_193), 0},
- {(char *)"qqual", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_194), 0},
- {(char *)"qstart", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_195), 0},
- {(char *)"qend", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_196), 0},
- {(char *)"qlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_197), 0},
- {(char *)"tags", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tags, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_198), 0},
- {(char *)"flag", __pyx_getprop_5pysam_9csamtools_11AlignedRead_flag, __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_199), 0},
- {(char *)"rname", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rname, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_200), 0},
- {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tid, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0},
- {(char *)"pos", __pyx_getprop_5pysam_9csamtools_11AlignedRead_pos, __pyx_setprop_5pysam_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_202), 0},
- {(char *)"bin", __pyx_getprop_5pysam_9csamtools_11AlignedRead_bin, __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_203), 0},
- {(char *)"rlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_204), 0},
- {(char *)"aend", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_205), 0},
- {(char *)"alen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
- {(char *)"mapq", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mapq, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_207), 0},
- {(char *)"mrnm", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mrnm, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_208), 0},
- {(char *)"rnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_209), 0},
- {(char *)"mpos", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_210), 0},
- {(char *)"pnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_211), 0},
- {(char *)"isize", __pyx_getprop_5pysam_9csamtools_11AlignedRead_isize, __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_212), 0},
- {(char *)"tlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_213), 0},
- {(char *)"is_paired", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_214), 0},
- {(char *)"is_proper_pair", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_215), 0},
- {(char *)"is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_216), 0},
- {(char *)"mate_is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_217), 0},
- {(char *)"is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_218), 0},
- {(char *)"mate_is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_219), 0},
- {(char *)"is_read1", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_220), 0},
- {(char *)"is_read2", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_221), 0},
- {(char *)"is_secondary", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_222), 0},
- {(char *)"is_qcfail", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_223), 0},
- {(char *)"is_duplicate", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_224), 0},
- {(char *)"positions", __pyx_getprop_5pysam_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_225), 0},
- {(char *)"aligned_pairs", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_226), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_AlignedRead[] = {
+ {(char *)"qname", __pyx_getprop_9csamtools_11AlignedRead_qname, __pyx_setprop_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_188), 0},
+ {(char *)"cigar", __pyx_getprop_9csamtools_11AlignedRead_cigar, __pyx_setprop_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_189), 0},
+ {(char *)"cigarstring", __pyx_getprop_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_190), 0},
+ {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_191), 0},
+ {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_192), 0},
+ {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_193), 0},
+ {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_194), 0},
+ {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_195), 0},
+ {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_196), 0},
+ {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_197), 0},
+ {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_198), 0},
+ {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_199), 0},
+ {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_200), 0},
+ {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_202), 0},
+ {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_203), 0},
+ {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_204), 0},
+ {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_205), 0},
+ {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
+ {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_207), 0},
+ {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_208), 0},
+ {(char *)"rnext", __pyx_getprop_9csamtools_11AlignedRead_rnext, __pyx_setprop_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_209), 0},
+ {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_210), 0},
+ {(char *)"pnext", __pyx_getprop_9csamtools_11AlignedRead_pnext, __pyx_setprop_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_211), 0},
+ {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_212), 0},
+ {(char *)"tlen", __pyx_getprop_9csamtools_11AlignedRead_tlen, __pyx_setprop_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_213), 0},
+ {(char *)"is_paired", __pyx_getprop_9csamtools_11AlignedRead_is_paired, __pyx_setprop_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_214), 0},
+ {(char *)"is_proper_pair", __pyx_getprop_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_215), 0},
+ {(char *)"is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_216), 0},
+ {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_217), 0},
+ {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_218), 0},
+ {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_219), 0},
+ {(char *)"is_read1", __pyx_getprop_9csamtools_11AlignedRead_is_read1, __pyx_setprop_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_220), 0},
+ {(char *)"is_read2", __pyx_getprop_9csamtools_11AlignedRead_is_read2, __pyx_setprop_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_221), 0},
+ {(char *)"is_secondary", __pyx_getprop_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_222), 0},
+ {(char *)"is_qcfail", __pyx_getprop_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_223), 0},
+ {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_224), 0},
+ {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_225), 0},
+ {(char *)"aligned_pairs", __pyx_getprop_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_226), 0},
{0, 0, 0, 0, 0}
};
@@ -36018,12 +33503,12 @@ static PyBufferProcs __pyx_tp_as_buffer_AlignedRead = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_AlignedRead = {
+static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.AlignedRead"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_AlignedRead), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.AlignedRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_AlignedRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_AlignedRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36036,9 +33521,9 @@ static PyTypeObject __pyx_type_5pysam_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_5pysam_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/
+ __pyx_pf_9csamtools_11AlignedRead_4__hash__, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_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*/
@@ -36050,17 +33535,17 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_AlignedRead = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_AlignedRead, /*tp_methods*/
+ __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_AlignedRead, /*tp_getset*/
+ __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_AlignedRead, /*tp_new*/
+ __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36073,26 +33558,26 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_AlignedRead = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile __pyx_vtable_5pysam_9csamtools_Samfile;
+static struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_Samfile *p;
+static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_Samfile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Samfile;
- if (__pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_Samfile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
+ if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_Samfile(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_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);
@@ -36100,70 +33585,70 @@ static void __pyx_tp_dealloc_5pysam_9csamtools_Samfile(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_filename(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_nreferences(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_references(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_lengths(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_mapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_text(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_header(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_2_isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_4_hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_6_open)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_8gettid)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_10getrname)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_12_parseRegion)},
- {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_14reset)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_17seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_16seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_19tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_18tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_21fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_20fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_23mate, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_22mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_25count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_24count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_27pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_26pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_29close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_28close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_32write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_34__enter__)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_36__exit__)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_38_buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_42__next__)},
+static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
+ {__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}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Samfile[] = {
- {(char *)"filename", __pyx_getprop_5pysam_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
- {(char *)"nreferences", __pyx_getprop_5pysam_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_227), 0},
- {(char *)"references", __pyx_getprop_5pysam_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_228), 0},
- {(char *)"lengths", __pyx_getprop_5pysam_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_229), 0},
- {(char *)"mapped", __pyx_getprop_5pysam_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_230), 0},
- {(char *)"unmapped", __pyx_getprop_5pysam_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_231), 0},
- {(char *)"text", __pyx_getprop_5pysam_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_232), 0},
- {(char *)"header", __pyx_getprop_5pysam_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_233), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
+ {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
+ {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_227), 0},
+ {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_228), 0},
+ {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_229), 0},
+ {(char *)"mapped", __pyx_getprop_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_230), 0},
+ {(char *)"unmapped", __pyx_getprop_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_231), 0},
+ {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_232), 0},
+ {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_233), 0},
{0, 0, 0, 0, 0}
};
@@ -36265,12 +33750,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = {
+static PyTypeObject __pyx_type_9csamtools_Samfile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.Samfile"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_Samfile), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_Samfile, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36295,11 +33780,11 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_7Samfile_41__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_7Samfile_43__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_Samfile, /*tp_methods*/
+ __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_5pysam_9csamtools_Samfile, /*tp_getset*/
+ __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -36307,7 +33792,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_Samfile, /*tp_new*/
+ __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36321,27 +33806,27 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupProxy(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_tid(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o);
}
-static int __pyx_setprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
+static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(o, v);
+ return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -36349,23 +33834,23 @@ static int __pyx_setprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, PyObject
}
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupProxy[] = {
+static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupProxy[] = {
- {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
- {(char *)"n", __pyx_getprop_5pysam_9csamtools_11PileupProxy_n, __pyx_setprop_5pysam_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_235), 0},
- {(char *)"pos", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pos, 0, 0, 0},
- {(char *)"pileups", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_236), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
+ {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_235), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
+ {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_236), 0},
{0, 0, 0, 0, 0}
};
@@ -36467,12 +33952,12 @@ static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_PileupProxy = {
+static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.PileupProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_PileupProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36487,7 +33972,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_PileupProxy = {
&__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_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*/
@@ -36499,17 +33984,17 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_PileupProxy = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_PileupProxy, /*tp_methods*/
+ __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_PileupProxy, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_PileupProxy, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36523,79 +34008,79 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_PileupProxy = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupRead(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p;
+static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_PileupRead *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_PileupRead *)o);
- p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ p = ((struct __pyx_obj_9csamtools_PileupRead *)o);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
- Py_CLEAR(p->_alignment);
+static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ Py_XDECREF(((PyObject *)p->_alignment));
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
if (p->_alignment) {
e = (*v)(((PyObject*)p->_alignment), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
+static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
PyObject* tmp;
tmp = ((PyObject*)p->_alignment);
- p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_alignment(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_qpos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_indel(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_del(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_head(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_level(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupRead[] = {
+static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupRead[] = {
- {(char *)"alignment", __pyx_getprop_5pysam_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_237), 0},
- {(char *)"qpos", __pyx_getprop_5pysam_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
- {(char *)"indel", __pyx_getprop_5pysam_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
- {(char *)"is_del", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
- {(char *)"is_head", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_head, 0, 0, 0},
- {(char *)"is_tail", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail, 0, 0, 0},
- {(char *)"level", __pyx_getprop_5pysam_9csamtools_10PileupRead_level, 0, 0, 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = {
+ {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_237), 0},
+ {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
+ {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
+ {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
+ {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0},
+ {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0},
+ {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0},
{0, 0, 0, 0, 0}
};
@@ -36697,12 +34182,12 @@ static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_PileupRead = {
+static PyTypeObject __pyx_type_9csamtools_PileupRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.PileupRead"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_PileupRead), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_PileupRead, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_PileupRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36717,29 +34202,29 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_PileupRead = {
&__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_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*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_PileupRead, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_PileupRead, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_PileupRead, /*tp_methods*/
+ __pyx_methods_9csamtools_PileupRead, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_PileupRead, /*tp_getset*/
+ __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_PileupRead, /*tp_new*/
+ __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36753,17 +34238,17 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_PileupRead = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRow(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRow[] = {
+static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
{0, 0, 0, 0}
};
@@ -36865,12 +34350,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRow = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRow"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRow), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRow, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36897,7 +34382,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRow, /*tp_methods*/
+ __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -36907,7 +34392,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRow, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRow, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36920,58 +34405,62 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion __pyx_vtable_5pysam_9csamtools_IteratorRowRegion;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) {
+ 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_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_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);
}
- Py_CLEAR(p->samfile);
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+ Py_XDECREF(((PyObject *)p->samfile));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
- e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion)); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->samfile) {
e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
+ {__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}
};
@@ -37073,12 +34562,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -37099,13 +34588,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = {
&__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each [...]
- __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowRegion, /*tp_methods*/
+ __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*/
0, /*tp_base*/
@@ -37115,7 +34604,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowRegion, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -37128,35 +34617,35 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll __pyx_vtable_5pysam_9csamtools_IteratorRowAll;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAll *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
- if (__pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
+ if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_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);
}
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAll[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
+ {__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}
};
@@ -37258,12 +34747,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowAll"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -37288,9 +34777,9 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowAll, /*tp_methods*/
+ __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*/
0, /*tp_base*/
@@ -37300,7 +34789,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowAll, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -37314,30 +34803,32 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
- Py_CLEAR(p->samfile);
- Py_CLEAR(p->rowiter);
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->rowiter));
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
- e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs)); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->samfile) {
e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
@@ -37347,22 +34838,24 @@ static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o, v
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->rowiter);
- p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
+ {__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}
};
@@ -37464,12 +34957,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -37490,13 +34983,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = {
&__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs, /*tp_methods*/
+ __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*/
0, /*tp_base*/
@@ -37506,7 +34999,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -37519,58 +35012,62 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection __pyx_vtable_5pysam_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
+ 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_5pysam_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;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_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);
}
- Py_CLEAR(p->positions);
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+ Py_XDECREF(p->positions);
+ __pyx_tp_dealloc_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
- e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection)); if (e) return e;
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
+ e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->positions) {
e = (*v)(p->positions, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
+static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection);
+ if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
+ __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
+ }
tmp = ((PyObject*)p->positions);
p->positions = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowSelection[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
+ {__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}
};
@@ -37672,12 +35169,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = {
+static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorRowSelection"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -37698,13 +35195,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = {
&__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/
- __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorRowSelection, /*tp_methods*/
+ __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*/
0, /*tp_base*/
@@ -37714,7 +35211,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorRowSelection, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -37727,45 +35224,45 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_vtable_5pysam_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p;
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o);
- p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
- p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
+ p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ 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_5pysam_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;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_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);
}
- Py_CLEAR(p->iter);
- Py_CLEAR(p->samfile);
- Py_CLEAR(p->fastafile);
- Py_CLEAR(p->stepper);
+ Py_XDECREF(((PyObject *)p->iter));
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(((PyObject *)p->fastafile));
+ Py_XDECREF(p->stepper);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
if (p->iter) {
e = (*v)(((PyObject*)p->iter), a); if (e) return e;
}
@@ -37781,17 +35278,17 @@ static int __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn(PyObject *o, visit
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
PyObject* tmp;
tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->fastafile);
- p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->stepper);
p->stepper = Py_None; Py_INCREF(Py_None);
@@ -37799,18 +35296,18 @@ static int __pyx_tp_clear_5pysam_9csamtools_IteratorColumn(PyObject *o) {
return 0;
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_4addReference)},
- {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_6hasReference)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
+ {__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}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_IteratorColumn[] = {
- {(char *)"seq_len", __pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
+ {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
{0, 0, 0, 0, 0}
};
@@ -37912,12 +35409,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumn = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorColumn"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumn), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -37938,15 +35435,15 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumn = {
&__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n\n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will conta [...]
- __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorColumn, /*tp_methods*/
+ __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_IteratorColumn, /*tp_getset*/
+ __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -37954,7 +35451,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumn = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorColumn, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -37967,22 +35464,22 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumn = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnRegion *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
- if (__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
+ if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
+ {__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}
};
@@ -38084,12 +35581,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnRegion = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorColumnRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -38110,17 +35607,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnRegion = {
&__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
- #else
0, /*tp_iter*/
- #endif
- __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorColumnRegion, /*tp_methods*/
+ __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -38130,7 +35623,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnRegion = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -38143,22 +35636,22 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnRegion = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs __pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs;
+static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *p;
- PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p;
+ PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
- if (__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
+ if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__)},
+static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
+ {__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}
};
@@ -38260,12 +35753,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs = {
+static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IteratorColumnAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -38286,17 +35779,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs = {
&__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
- #else
0, /*tp_iter*/
- #endif
- __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
+ __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/
+ __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -38306,7 +35795,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_new*/
+ __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -38320,35 +35809,35 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_IndexedReads(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p;
+static PyObject *__pyx_tp_new_9csamtools_IndexedReads(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_9csamtools_IndexedReads *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p = ((struct __pyx_obj_9csamtools_IndexedReads *)o);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
p->index = Py_None; Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_5pysam_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);
}
- Py_CLEAR(p->samfile);
- Py_CLEAR(p->index);
+ Py_XDECREF(((PyObject *)p->samfile));
+ Py_XDECREF(p->index);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
if (p->samfile) {
e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
@@ -38358,11 +35847,11 @@ static int __pyx_tp_traverse_5pysam_9csamtools_IndexedReads(PyObject *o, visitpr
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools_IndexedReads(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
PyObject* tmp;
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->index);
p->index = Py_None; Py_INCREF(Py_None);
@@ -38370,9 +35859,9 @@ static int __pyx_tp_clear_5pysam_9csamtools_IndexedReads(PyObject *o) {
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_IndexedReads[] = {
- {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_3build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_2build)},
- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_4find)},
+static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = {
+ {__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}
};
@@ -38474,12 +35963,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_IndexedReads = {
+static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.IndexedReads"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_IndexedReads), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_IndexedReads, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -38500,13 +35989,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IndexedReads = {
&__pyx_tp_as_buffer_IndexedReads, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools_IndexedReads, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools_IndexedReads, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools_IndexedReads, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools_IndexedReads, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_IndexedReads, /*tp_methods*/
+ __pyx_methods_9csamtools_IndexedReads, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -38514,9 +36003,9 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IndexedReads = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_IndexedReads, /*tp_new*/
+ __pyx_tp_new_9csamtools_IndexedReads, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -38530,61 +36019,61 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IndexedReads = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools_SNPCall(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools_SNPCall(PyObject *o) {
+static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_tid(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_3tid_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_pos(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_3pos_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_reference_base(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_14reference_base_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_genotype(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_8genotype_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_consensus_quality(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_17consensus_quality_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_snp_quality(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_11snp_quality_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_mapping_quality(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_15mapping_quality_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o);
}
-static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_coverage(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_9csamtools_7SNPCall_8coverage_1__get__(o);
+static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
+ return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools_SNPCall[] = {
+static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_SNPCall[] = {
- {(char *)"tid", __pyx_getprop_5pysam_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
- {(char *)"pos", __pyx_getprop_5pysam_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
- {(char *)"reference_base", __pyx_getprop_5pysam_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
- {(char *)"genotype", __pyx_getprop_5pysam_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
- {(char *)"consensus_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
- {(char *)"snp_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_246), 0},
- {(char *)"mapping_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_247), 0},
- {(char *)"coverage", __pyx_getprop_5pysam_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_248), 0},
+static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
+ {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
+ {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
+ {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
+ {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
+ {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_246), 0},
+ {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_247), 0},
+ {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_248), 0},
{0, 0, 0, 0, 0}
};
@@ -38686,12 +36175,12 @@ static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools_SNPCall = {
+static PyTypeObject __pyx_type_9csamtools_SNPCall = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.SNPCall"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools_SNPCall), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_SNPCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -38706,7 +36195,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_SNPCall = {
&__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_5pysam_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*/
@@ -38718,9 +36207,9 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_SNPCall = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools_SNPCall, /*tp_methods*/
+ __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_5pysam_9csamtools_SNPCall, /*tp_getset*/
+ __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -38728,7 +36217,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_SNPCall = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_SNPCall, /*tp_new*/
+ __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -38742,11 +36231,221 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_SNPCall = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p;
+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_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o);
+ 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 = __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;
p->__pyx_v_y = 0;
p->__pyx_t_0 = 0;
@@ -38754,18 +36453,19 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr(PyTy
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
- Py_CLEAR(p->__pyx_v_x);
- Py_CLEAR(p->__pyx_v_y);
- Py_CLEAR(p->__pyx_t_0);
- Py_CLEAR(p->__pyx_t_1);
- (*Py_TYPE(o)->tp_free)(o);
+static void __pyx_tp_dealloc_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;
+ Py_XDECREF(p->__pyx_v_x);
+ Py_XDECREF(p->__pyx_v_y);
+ Py_XDECREF(p->__pyx_t_0);
+ Py_XDECREF(p->__pyx_t_1);
+ __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
+ 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;
}
@@ -38781,9 +36481,10 @@ static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObj
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)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);
@@ -38799,7 +36500,7 @@ static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr[] = {
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct__genexpr[] = {
{0, 0, 0, 0}
};
@@ -38901,12 +36602,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__genexpr = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -38927,13 +36628,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
&__pyx_tp_as_buffer___pyx_scope_struct__genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
+ __pyx_methods_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
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0, /*tp_getset*/
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0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
+ __pyx_tp_new_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
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#endif
};
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- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+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 = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o);
+ p = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o);
p->__pyx_v_x = 0;
p->__pyx_v_y = 0;
p->__pyx_t_0 = 0;
@@ -38969,18 +36670,19 @@ static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyT
return o;
}
-static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
- Py_CLEAR(p->__pyx_v_x);
- Py_CLEAR(p->__pyx_v_y);
- Py_CLEAR(p->__pyx_t_0);
- Py_CLEAR(p->__pyx_t_1);
- (*Py_TYPE(o)->tp_free)(o);
+static void __pyx_tp_dealloc_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;
+ Py_XDECREF(p->__pyx_v_x);
+ Py_XDECREF(p->__pyx_v_y);
+ Py_XDECREF(p->__pyx_t_0);
+ Py_XDECREF(p->__pyx_t_1);
+ __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
}
-static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ 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;
}
@@ -38996,9 +36698,10 @@ static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyOb
return 0;
}
-static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)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);
@@ -39014,7 +36717,7 @@ static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObjec
return 0;
}
-static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr[] = {
+static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr[] = {
{0, 0, 0, 0}
};
@@ -39116,12 +36819,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
#endif
};
-static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr = {
+static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct_1_genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -39142,13 +36845,13 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr =
&__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
- __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
+ __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
+ __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -39158,7 +36861,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr =
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0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
+ __pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
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{&__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},
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{&__pyx_kp_s_256, __pyx_k_256, sizeof(__pyx_k_256), 0, 0, 1, 0},
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{&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
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{&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
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{&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
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{&__pyx_n_s___samtools_dispatch, __pyx_k___samtools_dispatch, sizeof(__pyx_k___samtools_dispatch), 0, 0, 1, 1},
- {&__pyx_n_s__a, __pyx_k__a, sizeof(__pyx_k__a), 0, 0, 1, 1},
{&__pyx_n_s__add_sq_text, __pyx_k__add_sq_text, sizeof(__pyx_k__add_sq_text), 0, 0, 1, 1},
{&__pyx_n_s__alignment, __pyx_k__alignment, sizeof(__pyx_k__alignment), 0, 0, 1, 1},
{&__pyx_n_s__all, __pyx_k__all, sizeof(__pyx_k__all), 0, 0, 1, 1},
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{&__pyx_n_s__calcsize, __pyx_k__calcsize, sizeof(__pyx_k__calcsize), 0, 0, 1, 1},
{&__pyx_n_s__callback, __pyx_k__callback, sizeof(__pyx_k__callback), 0, 0, 1, 1},
- {&__pyx_n_s__cargs, __pyx_k__cargs, sizeof(__pyx_k__cargs), 0, 0, 1, 1},
{&__pyx_n_s__catch_stdout, __pyx_k__catch_stdout, sizeof(__pyx_k__catch_stdout), 0, 0, 1, 1},
{&__pyx_n_s__check_header, __pyx_k__check_header, sizeof(__pyx_k__check_header), 0, 0, 1, 1},
{&__pyx_n_s__check_sq, __pyx_k__check_sq, sizeof(__pyx_k__check_sq), 0, 0, 1, 1},
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{&__pyx_n_s__consensus_quality, __pyx_k__consensus_quality, sizeof(__pyx_k__consensus_quality), 0, 0, 1, 1},
{&__pyx_n_s__coverage, __pyx_k__coverage, sizeof(__pyx_k__coverage), 0, 0, 1, 1},
+ {&__pyx_n_s__csamtools, __pyx_k__csamtools, sizeof(__pyx_k__csamtools), 0, 0, 1, 1},
{&__pyx_n_s__ctypes, __pyx_k__ctypes, sizeof(__pyx_k__ctypes), 0, 0, 1, 1},
{&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1},
{&__pyx_n_s__data_len, __pyx_k__data_len, sizeof(__pyx_k__data_len), 0, 0, 1, 1},
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{&__pyx_n_s__indel, __pyx_k__indel, sizeof(__pyx_k__indel), 0, 0, 1, 1},
{&__pyx_n_s__index, __pyx_k__index, sizeof(__pyx_k__index), 0, 0, 1, 1},
- {&__pyx_n_s__inf, __pyx_k__inf, sizeof(__pyx_k__inf), 0, 0, 1, 1},
{&__pyx_n_s__is_del, __pyx_k__is_del, sizeof(__pyx_k__is_del), 0, 0, 1, 1},
{&__pyx_n_s__is_head, __pyx_k__is_head, sizeof(__pyx_k__is_head), 0, 0, 1, 1},
{&__pyx_n_s__is_tail, __pyx_k__is_tail, sizeof(__pyx_k__is_tail), 0, 0, 1, 1},
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{&__pyx_n_s__object, __pyx_k__object, sizeof(__pyx_k__object), 0, 0, 1, 1},
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{&__pyx_n_s__ord, __pyx_k__ord, sizeof(__pyx_k__ord), 0, 0, 1, 1},
{&__pyx_n_s__os, __pyx_k__os, sizeof(__pyx_k__os), 0, 0, 1, 1},
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{&__pyx_n_s__pack_into, __pyx_k__pack_into, sizeof(__pyx_k__pack_into), 0, 0, 1, 1},
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{&__pyx_n_s__restore, __pyx_k__restore, sizeof(__pyx_k__restore), 0, 0, 1, 1},
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
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__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
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- __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)", 0);
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if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #ifdef __pyx_binding_PyCFunctionType_USED
+ if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
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- #if PY_MAJOR_VERSION >= 3
- {
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- if (!PyDict_GetItemString(modules, "pysam.csamtools")) {
- if (unlikely(PyDict_SetItemString(modules, "pysam.csamtools", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
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+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+ if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
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- if (__pyx_module_is_main_pysam__csamtools) {
+ if (__pyx_module_is_main_csamtools) {
if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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/*--- Builtin init code ---*/
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/*--- Global init code ---*/
- __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- __pyx_vtabptr_5pysam_9csamtools_Fastafile = &__pyx_vtable_5pysam_9csamtools_Fastafile;
- __pyx_vtable_5pysam_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_5pysam_9csamtools_9Fastafile__fetch;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_Fastafile = &__pyx_type_5pysam_9csamtools_Fastafile;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
+ __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
+ if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
+ if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__.doc = __pyx_doc_5pysam_9csamtools_11AlignedRead_4__str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__;
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- }
- #endif
- if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_AlignedRead = &__pyx_type_5pysam_9csamtools_AlignedRead;
- __pyx_vtabptr_5pysam_9csamtools_Samfile = &__pyx_vtable_5pysam_9csamtools_Samfile;
- __pyx_vtable_5pysam_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *))__pyx_f_5pysam_9csamtools_7Samfile__buildHeader;
- __pyx_vtable_5pysam_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_getCurrent;
- __pyx_vtable_5pysam_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_cnext;
- __pyx_vtable_5pysam_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_5pysam_9csamtools_7Samfile_write;
- __pyx_vtable_5pysam_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int))__pyx_f_5pysam_9csamtools_7Samfile__getrname;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __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;}
+ __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
+ __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
+ __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
+ __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
+ __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
+ __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
+ __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname;
+ if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__.doc = __pyx_doc_5pysam_9csamtools_7Samfile_42__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__;
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- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Samfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_Samfile = &__pyx_type_5pysam_9csamtools_Samfile;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_PileupProxy = &__pyx_type_5pysam_9csamtools_PileupProxy;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_PileupRead = &__pyx_type_5pysam_9csamtools_PileupRead;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRow = &__pyx_type_5pysam_9csamtools_IteratorRow;
- __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion = &__pyx_vtable_5pysam_9csamtools_IteratorRowRegion;
- __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_getCurrent;
- __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_cnext;
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+ __pyx_wrapperbase_9csamtools_7Samfile_21__next__.doc = __pyx_doc_9csamtools_7Samfile_21__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_21__next__;
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+ 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;}
+ if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
+ if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
+ __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
+ __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
+ __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__.doc = __pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowRegion = &__pyx_type_5pysam_9csamtools_IteratorRowRegion;
- __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll = &__pyx_vtable_5pysam_9csamtools_IteratorRowAll;
- __pyx_vtable_5pysam_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_getCurrent;
- __pyx_vtable_5pysam_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_cnext;
- __pyx_type_5pysam_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __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;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
+ __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll;
+ __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
+ __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__.doc = __pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_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__;
}
}
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowAll = &__pyx_type_5pysam_9csamtools_IteratorRowAll;
- __pyx_type_5pysam_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ 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;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
+ __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__.doc = __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
- }
- }
- #endif
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = &__pyx_type_5pysam_9csamtools_IteratorRowAllRefs;
- __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection = &__pyx_vtable_5pysam_9csamtools_IteratorRowSelection;
- __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_getCurrent;
- __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_cnext;
- __pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __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;}
+ __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
+ __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
+ __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
+ __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
+ __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorRowSelection = &__pyx_type_5pysam_9csamtools_IteratorRowSelection;
- __pyx_vtabptr_5pysam_9csamtools_IteratorColumn = &__pyx_vtable_5pysam_9csamtools_IteratorColumn;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_cnext;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_getSequence;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_setMask;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_5pysam_9csamtools_14IteratorColumn_setupIteratorData;
- __pyx_vtable_5pysam_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_reset;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorColumn = &__pyx_type_5pysam_9csamtools_IteratorColumn;
- __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion = &__pyx_vtable_5pysam_9csamtools_IteratorColumnRegion;
- __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
- __pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __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;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
+ __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
+ __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
+ __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence;
+ __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
+ __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
+ __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
+ __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
+ __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
+ __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
+ if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
- }
- }
- #endif
- if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = &__pyx_type_5pysam_9csamtools_IteratorColumnRegion;
- __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs;
- __pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
- __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
+ __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;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/*--- Function import code ---*/
/*--- Execution code ---*/
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@@ -41714,17 +39090,17 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
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+ /* "csamtools.pyx":142
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@@ -41754,7 +39130,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
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@@ -41763,25 +39139,25 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*/
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return py_code;
}
-#endif /* CYTHON_PROFILE */
-static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
- const char* cstring, Py_ssize_t start, Py_ssize_t stop,
- const char* encoding, const char* errors,
- PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
- Py_ssize_t length;
- if (unlikely((start < 0) | (stop < 0))) {
- length = strlen(cstring);
- if (start < 0) {
- start += length;
- if (start < 0)
- start = 0;
- }
- if (stop < 0)
- stop += length;
- }
- length = stop - start;
- if (unlikely(length <= 0))
- return PyUnicode_FromUnicode(NULL, 0);
- cstring += start;
- if (decode_func) {
- return decode_func(cstring, length, errors);
- } else {
- return PyUnicode_Decode(cstring, length, encoding, errors);
- }
-}
+#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;
@@ -42569,60 +39925,55 @@ 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);
- if (!value || value == Py_None)
- value = NULL;
- else
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ /* Next, replace a missing value with None */
+ if (value == NULL) {
+ value = Py_None;
Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
}
#if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
+ if (!PyClass_Check(type))
#else
- if (PyType_Check(type)) {
+ if (!PyType_Check(type))
#endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
+ {
+ /* Raising an instance. The value should be a dummy. */
+ if (value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
+ /* Normalize to raise <class>, <instance> */
+ Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -42645,6 +39996,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
}
#endif
}
+
__Pyx_ErrRestore(type, value, tb);
return;
raise_error:
@@ -42653,9 +40005,10 @@ raise_error:
Py_XDECREF(tb);
return;
}
+
#else /* Python 3+ */
+
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -42665,6 +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,
@@ -42673,36 +40027,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
+ } else if (!PyExceptionClass_Check(type)) {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause && cause != Py_None) {
+
+ if (cause) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -42719,9 +40050,14 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
+ if (!value) {
+ value = PyObject_CallObject(type, NULL);
+ }
PyException_SetCause(value, fixed_cause);
}
+
PyErr_SetObject(type, value);
+
if (tb) {
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
@@ -42731,8 +40067,8 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
Py_XDECREF(tmp_tb);
}
}
+
bad:
- Py_XDECREF(owned_instance);
return;
}
#endif
@@ -42756,17 +40092,13 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
{
PyObject* key = 0;
Py_ssize_t pos = 0;
-#if CPYTHON_COMPILING_IN_PYPY
- if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
- goto invalid_keyword;
- return 1;
-#else
while (PyDict_Next(kwdict, &pos, &key, 0)) {
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
#endif
- if (unlikely(!PyUnicode_Check(key)))
- goto invalid_keyword_type;
+ goto invalid_keyword_type;
}
if ((!kw_allowed) && unlikely(key))
goto invalid_keyword;
@@ -42775,7 +40107,6 @@ invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
"%s() keywords must be strings", function_name);
return 0;
-#endif
invalid_keyword:
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION < 3
@@ -42797,7 +40128,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
+ PyString_AS_STRING(kw_name));
#endif
}
@@ -42813,77 +40144,55 @@ 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++;
if (*name) {
values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
}
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
+ if (*name) {
values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
+ } else {
+ /* unexpected keyword found */
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
}
}
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -42911,6 +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";
@@ -42922,7 +40232,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -42949,7 +40259,6 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -42958,27 +40267,19 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
*type = local_type;
*value = local_value;
*tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
+ Py_INCREF(local_type);
+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -42986,13 +40287,10 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
+ these objects (XDECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
return 0;
bad:
*type = 0;
@@ -43004,40 +40302,25 @@ bad:
return -1;
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
index, (index == 1) ? "" : "s");
}
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+}
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ } else if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
PyErr_Clear();
return 0;
@@ -43046,18 +40329,10 @@ static CYTHON_INLINE int __Pyx_IterFinish(void) {
}
}
return 0;
-#endif
}
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
}
static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
@@ -43077,25 +40352,8 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
}
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_base && type->tp_base->tp_traverse)
- return type->tp_base->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_base && type->tp_base->tp_clear)
- type->tp_base->tp_clear(obj);
-}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -43103,12 +40361,9 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
}
+
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -43120,9 +40375,6 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
@@ -43151,33 +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) {
@@ -43196,6 +40427,7 @@ bad:
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
+ /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -43223,8 +40455,11 @@ 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) {
Py_INCREF(metaclass);
@@ -43236,526 +40471,105 @@ 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;
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-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;
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-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;
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- Py_INCREF(op->func_dict);
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-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;
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- if (op->defaults_getter) {
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- Py_INCREF(res);
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- return res;
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- Py_INCREF(Py_None);
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- {(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}
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-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
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-#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}
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- 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;
+ 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;
-}
-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("<cyfunction %U at %p>",
- func_name, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(func_name), (void *)op);
-#endif
-}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
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- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
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- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
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- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
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- break;
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- if (size == 1)
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- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
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- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
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- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
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-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
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- 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_CyFunction_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
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-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
- 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;
-}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, sizeof(size));
- m->defaults_pyobjects = pyobjects;
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-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
+
}
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
- const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint64_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
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- return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint64_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
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- return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
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- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
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- } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
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- PyErr_SetString(PyExc_RuntimeError,
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- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+ 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)) {
+ return (equals == Py_NE);
+ } else if (PyBytes_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
+ else
+ return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
+ } else {
+ int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
}
- #endif
- return (uint64_t)-1;
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
}
}
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
- const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint32_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint32_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
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- return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
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- if (is_unsigned)
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- return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
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- return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
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- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+ 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 (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyUnicode_AS_UNICODE(s1)[0] == PyUnicode_AS_UNICODE(s2)[0]);
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+ return (PyUnicode_AS_UNICODE(s1)[0] != PyUnicode_AS_UNICODE(s2)[0]);
+ } else {
+ int result = PyUnicode_Compare(s1, s2);
+ if ((result == -1) && unlikely(PyErr_Occurred()))
+ return -1;
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
}
- #endif
- return (uint32_t)-1;
+ } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
}
}
@@ -43909,6 +40723,58 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
}
}
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
+ const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint32_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint32_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint32_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint32_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint32_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ return (uint32_t)-1;
+ }
+}
+
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -43934,6 +40800,58 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
}
}
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
+ const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint64_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint64_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint64_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint64_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ uint64_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ return (uint64_t)-1;
+ }
+}
+
static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -43963,10 +40881,6 @@ static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
else
return (uint8_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
uint8_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
@@ -43986,7 +40900,6 @@ static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
if (likely(!ret))
return val;
}
- #endif
return (uint8_t)-1;
}
}
@@ -44020,10 +40933,6 @@ 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
@@ -44043,7 +40952,6 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
if (likely(!ret))
return val;
}
- #endif
return (int32_t)-1;
}
}
@@ -44475,526 +41383,129 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
+
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
+
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
+
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
}
-static PyObject *__Pyx_Generator_Next(PyObject *self);
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
-static PyObject *__Pyx_Generator_Close(PyObject *self);
-static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
-static PyTypeObject *__pyx_GeneratorType = 0;
-#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
-#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
- PyObject *et, *ev, *tb;
- PyObject *value = NULL;
- __Pyx_ErrFetch(&et, &ev, &tb);
- if (!et) {
- Py_XDECREF(tb);
- Py_XDECREF(ev);
- Py_INCREF(Py_None);
- *pvalue = Py_None;
- return 0;
- }
- if (unlikely(et != PyExc_StopIteration) &&
- unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- if (likely(et == PyExc_StopIteration)) {
- if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
- if (!ev) {
- Py_INCREF(Py_None);
- ev = Py_None;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
- *pvalue = ev;
- return 0;
- }
- }
- PyErr_NormalizeException(&et, &ev, &tb);
- if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
-#if PY_VERSION_HEX >= 0x030300A0
- value = ((PyStopIterationObject *)ev)->value;
- Py_INCREF(value);
- Py_DECREF(ev);
-#else
- {
- PyObject* args = PyObject_GetAttrString(ev, "args");
- Py_DECREF(ev);
- if (likely(args)) {
- value = PyObject_GetItem(args, 0);
- Py_DECREF(args);
- }
- if (unlikely(!value)) {
- __Pyx_ErrRestore(NULL, NULL, NULL);
- Py_INCREF(Py_None);
- value = Py_None;
- }
- }
-#endif
- *pvalue = value;
- return 0;
-}
-#endif
-static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
- PyObject *exc_type = self->exc_type;
- PyObject *exc_value = self->exc_value;
- PyObject *exc_traceback = self->exc_traceback;
+static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self)
+{
+ 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
-int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
- if (unlikely(gen->is_running)) {
+
+static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value)
+{
+ PyObject *retval;
+
+ if (self->is_running) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return 1;
+ return NULL;
}
- return 0;
-}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
- PyObject *retval;
- assert(!self->is_running);
- if (unlikely(self->resume_label == 0)) {
- if (unlikely(value && value != Py_None)) {
+
+ 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) {
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Generators always return to their most recent caller, not
- * necessarily their creator. */
- if (self->exc_traceback) {
- PyThreadState *tstate = PyThreadState_GET();
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_XINCREF(tstate->frame);
- assert(f->f_back == NULL);
- f->f_back = tstate->frame;
- }
-#endif
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
- &self->exc_traceback);
- } else {
+
+
+ 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);
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Don't keep the reference to f_back any longer than necessary. It
- * may keep a chain of frames alive or it could create a reference
- * cycle. */
- if (self->exc_traceback) {
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_CLEAR(f->f_back);
- }
-#endif
- } else {
+
+ if (retval)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
__Pyx_Generator_ExceptionClear(self);
- }
+
return retval;
}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
- PyObject *ret;
- PyObject *val = NULL;
- __Pyx_Generator_Undelegate(gen);
- __Pyx_PyGen_FetchStopIterationValue(&val);
- ret = __Pyx_Generator_SendEx(gen, val);
- Py_XDECREF(val);
- return ret;
-}
-static PyObject *__Pyx_Generator_Next(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- ret = Py_TYPE(yf)->tp_iternext(yf);
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, Py_None);
-}
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Send(yf, value);
- } else {
- if (value == Py_None)
- ret = PyIter_Next(yf);
- else
- ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
- }
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, value);
+
+static PyObject *__Pyx_Generator_Next(PyObject *self)
+{
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None);
}
-static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
- PyObject *retval = NULL;
- int err = 0;
- if (__Pyx_Generator_CheckExact(yf)) {
- retval = __Pyx_Generator_Close(yf);
- if (!retval)
- return -1;
- } else {
- PyObject *meth;
- gen->is_running = 1;
- meth = PyObject_GetAttrString(yf, "close");
- if (unlikely(!meth)) {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_WriteUnraisable(yf);
- }
- PyErr_Clear();
- } else {
- retval = PyObject_CallFunction(meth, NULL);
- Py_DECREF(meth);
- if (!retval)
- err = -1;
- }
- gen->is_running = 0;
- }
- Py_XDECREF(retval);
- return err;
+
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
+{
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value);
}
-static PyObject *__Pyx_Generator_Close(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject *retval, *raised_exception;
- PyObject *yf = gen->yieldfrom;
- int err = 0;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- Py_INCREF(yf);
- err = __Pyx_Generator_CloseIter(gen, yf);
- __Pyx_Generator_Undelegate(gen);
- Py_DECREF(yf);
- }
- if (err == 0)
+
+static PyObject *__Pyx_Generator_Close(PyObject *self)
+{
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
+ PyObject *retval;
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(gen, NULL);
+ retval = __Pyx_Generator_SendEx(generator, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
- raised_exception = PyErr_Occurred();
- if (!raised_exception
- || raised_exception == PyExc_StopIteration
-#if PY_VERSION_HEX >= 0x02050000
- || raised_exception == PyExc_GeneratorExit
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
+#if PY_VERSION_HEX < 0x02050000
+ if (PyErr_ExceptionMatches(PyExc_StopIteration))
+#else
+ if (PyErr_ExceptionMatches(PyExc_StopIteration)
+ || PyErr_ExceptionMatches(PyExc_GeneratorExit))
#endif
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- if (raised_exception) PyErr_Clear(); /* ignore these errors */
+ PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds)
+{
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
- PyObject *yf = gen->yieldfrom;
+
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- Py_INCREF(yf);
-#if PY_VERSION_HEX >= 0x02050000
- if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
- int err = __Pyx_Generator_CloseIter(gen, yf);
- Py_DECREF(yf);
- __Pyx_Generator_Undelegate(gen);
- if (err < 0)
- return __Pyx_Generator_SendEx(gen, NULL);
- goto throw_here;
- }
-#endif
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Throw(yf, args);
- } else {
- PyObject *meth = PyObject_GetAttrString(yf, "throw");
- if (unlikely(!meth)) {
- Py_DECREF(yf);
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- gen->is_running = 0;
- return NULL;
- }
- PyErr_Clear();
- __Pyx_Generator_Undelegate(gen);
- gen->is_running = 0;
- goto throw_here;
- }
- ret = PyObject_CallObject(meth, args);
- Py_DECREF(meth);
- }
- gen->is_running = 0;
- Py_DECREF(yf);
- if (!ret) {
- ret = __Pyx_Generator_FinishDelegation(gen);
- }
- return ret;
- }
-throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(gen, 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->yieldfrom);
- Py_VISIT(gen->exc_type);
- Py_VISIT(gen->exc_value);
- Py_VISIT(gen->exc_traceback);
- return 0;
-}
-static int __Pyx_Generator_clear(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->yieldfrom);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- return 0;
-}
-static void __Pyx_Generator_dealloc(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject_GC_UnTrack(gen);
- if (gen->gi_weakreflist != NULL)
- 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);
- __Pyx_Generator_clear(self);
- 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;
- }
-#if CYTHON_COMPILING_FOR_CPYTHON
- assert(PyType_IS_GC(self->ob_type) &&
- _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
- /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
- * we need to undo that. */
- _Py_DEC_REFTOTAL;
-#endif
- /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
- * chain, so no more to do there.
- * If COUNT_ALLOCS, the original decref bumped tp_frees, and
- * _Py_NewReference bumped tp_allocs: both of those need to be
- * undone.
- */
-#ifdef COUNT_ALLOCS
- --Py_TYPE(self)->tp_frees;
- --Py_TYPE(self)->tp_allocs;
-#endif
-}
-static PyMemberDef __pyx_Generator_memberlist[] = {
- {(char *) "gi_running",
-#if PY_VERSION_HEX >= 0x02060000
- T_BOOL,
-#else
- T_BYTE,
-#endif
- 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_type = {
- 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*/
- 0, /*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 */
- 0, /*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_type);
- 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->yieldfrom = 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) {
- __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
- __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
- if (PyType_Ready(&__pyx_GeneratorType_type)) {
- return -1;
- }
- __pyx_GeneratorType = &__pyx_GeneratorType_type;
- return 0;
+ return __Pyx_Generator_SendEx(generator, NULL);
}
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
- CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+ int lineno, const char *filename) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
@@ -45048,23 +41559,6 @@ bad:
return -1;
}
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -45074,10 +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);
@@ -45093,7 +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);
@@ -45103,7 +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);
@@ -45117,105 +41616,51 @@ 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);
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
}
+#endif
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-static 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 {
@@ -45226,45 +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,*/
@@ -45272,9 +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);
}
@@ -45309,7 +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/ctabix.c b/pysam/ctabix.c
index 2a1ce55..5846459 100644
--- a/pysam/ctabix.c
+++ b/pysam/ctabix.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.4 on Wed Jan 23 22:59:29 2013 */
+/* Generated by Cython 0.16 on Tue Jan 15 06:50:01 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -11,6 +11,7 @@
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
+
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -22,18 +23,22 @@
#define __fastcall
#endif
#endif
+
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
+
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
+
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
+
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
@@ -41,28 +46,28 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
+
+#if CYTHON_COMPILING_IN_PYPY
+ #define __Pyx_PyCFunction_Call PyObject_Call
+#else
+ #define __Pyx_PyCFunction_Call PyCFunction_Call
+#endif
+
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
+ #define 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"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -70,6 +75,7 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
+
typedef struct {
void *buf;
PyObject *obj;
@@ -83,6 +89,7 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
+
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -94,9 +101,11 @@
#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) \
@@ -106,30 +115,31 @@
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
+
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
+
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
+
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+
+
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -137,6 +147,7 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -155,6 +166,7 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -162,7 +174,9 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -179,9 +193,11 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
+
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -190,6 +206,7 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
+
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -208,9 +225,11 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -220,6 +239,7 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -228,7 +248,6 @@
#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)
@@ -317,11 +336,7 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
@@ -351,7 +366,6 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"ctabix.pyx",
"TabProxies.pxd",
- "type.pxd",
"bool.pxd",
"complex.pxd",
};
@@ -758,11 +772,6 @@ static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysa
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
-static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
- const char* cstring, Py_ssize_t start, Py_ssize_t stop,
- const char* encoding, const char* errors,
- PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
-
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -790,47 +799,42 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -846,39 +850,34 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
Py_INCREF(r);
return r;
}
- } else { /* inlined PySequence_GetItem() */
+ }
+ else if (likely(i >= 0)) {
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return NULL;
- i += l;
- }
return m->sq_item(o, i);
}
}
-#else
- if (PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
-
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
+ if (unlikely(d == Py_None)) {
+ __Pyx_RaiseNoneIndexingError();
+ return NULL;
+ }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -946,6 +945,16 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
PyObject *tuple);
static int __Pyx_CyFunction_init(void);
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
+
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
@@ -992,10 +1001,10 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
#endif
#endif
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
typedef struct {
@@ -1051,10 +1060,7 @@ static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0;
/* Module declarations from 'cpython.iterator' */
-/* Module declarations from '__builtin__' */
-
/* Module declarations from 'cpython.type' */
-static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
/* Module declarations from 'cpython.number' */
@@ -1213,7 +1219,7 @@ 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[] = "/ifs/devel/pysam/pysam/ctabix.pyx";
+static char __pyx_k_65[] = "/home/andreas/devel/pysam/pysam/ctabix.pyx";
static char __pyx_k_66[] = "pysam.ctabix";
static char __pyx_k_77[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
static char __pyx_k_80[] = "tabix_inplace_iterator";
@@ -1537,7 +1543,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
* return s[:length].decode("ascii")
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromStringAndSize(((const char*)__pyx_v_s) + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_s + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1554,7 +1560,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
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*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1951,7 +1957,7 @@ static PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *__pyx_v_s) {
* cdef _force_str(object s):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, strlen(__pyx_v_s), NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, strlen(__pyx_v_s), NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
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PyObject *__pyx_v_mode = 0;
PyObject *__pyx_v_args = 0;
PyObject *__pyx_v_kwargs = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
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__pyx_v_args = __pyx_empty_tuple; __Pyx_INCREF(__pyx_empty_tuple);
}
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
PyObject* values[2] = {0,0};
values[1] = ((PyObject *)__pyx_n_s__r);
if (unlikely(__pyx_kwds)) {
@@ -2135,7 +2141,8 @@ static int __pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -2313,11 +2320,11 @@ static char __pyx_doc_5pysam_6ctabix_9Tabixfile_4_open[] = "Tabixfile._open(self
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PyObject *__pyx_v_filename = 0;
PyObject *__pyx_v_mode = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_open (wrapper)", 0);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
PyObject* values[2] = {0,0};
values[1] = ((PyObject *)__pyx_n_s__r);
if (unlikely(__pyx_kwds)) {
@@ -2332,7 +2339,8 @@ static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_sel
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
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if (kw_args > 0) {
@@ -2381,8 +2389,8 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
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__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
int __pyx_t_5;
char *__pyx_t_6;
@@ -2404,11 +2412,9 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
#ifndef CYTHON_WITHOUT_ASSERTIONS
__Pyx_INCREF(__pyx_v_mode);
__pyx_t_1 = __pyx_v_mode;
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- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (unlikely(!((int)__pyx_t_3))) {
+ if (unlikely(!((int)__pyx_t_2))) {
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_5), __pyx_v_mode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_1));
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* self.tabixfile = NULL
*
*/
- __pyx_t_3 = (__pyx_v_self->tabixfile != NULL);
- if (__pyx_t_3) {
+ __pyx_t_2 = (__pyx_v_self->tabixfile != NULL);
+ if (__pyx_t_2) {
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
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- __Pyx_GOTREF(__pyx_t_2);
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+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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- __Pyx_GOTREF(__pyx_t_2);
- __pyx_v_filename_index = __pyx_t_2;
- __pyx_t_2 = 0;
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+ __Pyx_GOTREF(__pyx_t_3);
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+ __pyx_t_3 = 0;
/* "pysam/ctabix.pyx":112
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- __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyObject* values[4] = {0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
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+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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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;
@@ -4361,8 +4364,7 @@ static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5p
*
* if tid < 0:
*/
- __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
- __pyx_v_self->tabixfile = __pyx_t_4;
+ __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
/* "pysam/ctabix.pyx":293
* self.tabixfile = tabixfile.tabixfile
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/* Python wrapper */
static PyObject *__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__;
-#endif
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static int __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
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if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
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if (unlikely(kw_args > 0)) {
@@ -4723,7 +4724,6 @@ static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_
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;
@@ -4757,8 +4757,7 @@ static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_
*
* self.iterator = ti_query(self.tabixfile, NULL, 0, 0)
*/
- __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
- __pyx_v_self->tabixfile = __pyx_t_4;
+ __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
/* "pysam/ctabix.pyx":344
* self.tabixfile = tabixfile.tabixfile
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/* Python wrapper */
static PyObject *__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__;
-#endif
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char *__pyx_v_buffer;
int __pyx_v_len;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
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{
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if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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char *__pyx_v_buffer;
int __pyx_v_len;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
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{
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if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
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char *__pyx_v_buffer;
int __pyx_v_len;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
{
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if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -5368,11 +5371,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self
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char *__pyx_v_buffer;
int __pyx_v_len;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
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__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
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if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -5493,11 +5498,11 @@ static int __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__
int __pyx_v_start;
int __pyx_v_end;
struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__parser,0};
int __pyx_r;
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PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
+ values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser);
+ if (likely(values[4])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -5588,7 +5598,6 @@ static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_
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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;
@@ -5635,8 +5644,7 @@ static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_
*
* if tid < 0:
*/
- __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
- __pyx_v_self->tabixfile = __pyx_t_4;
+ __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
/* "pysam/ctabix.pyx":530
* self.tabixfile = tabixfile.tabixfile
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static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__;
-#endif
static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self) {
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PyObject *__pyx_v_filename_in = 0;
PyObject *__pyx_v_filename_out = 0;
PyObject *__pyx_v_force = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename_in,&__pyx_n_s__filename_out,&__pyx_n_s__force,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("tabix_compress (wrapper)", 0);
+ __pyx_self = __pyx_self;
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@@ -5964,10 +5971,12 @@ static PyObject *__pyx_pw_5pysam_6ctabix_1tabix_compress(PyObject *__pyx_self, P
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switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_in)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_in);
+ if (likely(values[0])) kw_args--;
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+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_out);
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else {
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PyObject *__pyx_v_preset = 0;
PyObject *__pyx_v_meta_char = 0;
PyObject *__pyx_v_zerobased = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__force,&__pyx_n_s__seq_col,&__pyx_n_s__start_col,&__pyx_n_s__end_col,&__pyx_n_s__preset,&__pyx_n_s__meta_char,&__pyx_n_s__zerobased,0};
PyObject *__pyx_r = 0;
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__Pyx_RefNannySetupContext("tabix_index (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
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switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -6605,19 +6616,23 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
* raise ValueError("neither preset nor seq_col,start_col and end_col given" )
*
*/
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+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_preset, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_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;
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- __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_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_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;
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- __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_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__pyx_t_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;
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@@ -7112,7 +7127,8 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
* preset = 0
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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@@ -7207,18 +7223,12 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
*/
if ((likely(PyTuple_CheckExact(__pyx_v_conf_data))) || (PyList_CheckExact(__pyx_v_conf_data))) {
PyObject* sequence = __pyx_v_conf_data;
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- Py_ssize_t size = Py_SIZE(sequence);
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- Py_ssize_t size = PySequence_Size(sequence);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
+ if (unlikely(PyTuple_GET_SIZE(sequence) != 6)) {
+ if (PyTuple_GET_SIZE(sequence) > 6) __Pyx_RaiseTooManyValuesError(6);
+ else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_14 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_15 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 2);
@@ -7226,6 +7236,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 4);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 5);
} else {
+ if (unlikely(PyList_GET_SIZE(sequence) != 6)) {
+ if (PyList_GET_SIZE(sequence) > 6) __Pyx_RaiseTooManyValuesError(6);
+ else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_14 = PyList_GET_ITEM(sequence, 0);
__pyx_t_15 = PyList_GET_ITEM(sequence, 1);
__pyx_t_9 = PyList_GET_ITEM(sequence, 2);
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__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_2);
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- for (i=0; i < 6; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- *(temps[i]) = item;
- }
- #endif
- } else
- {
+ } else {
Py_ssize_t index = -1;
- PyObject** temps[6] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_9,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2};
__pyx_t_16 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext;
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- PyObject* item = __pyx_t_17(__pyx_t_16); if (unlikely(!item)) goto __pyx_L20_unpacking_failed;
- __Pyx_GOTREF(item);
- *(temps[index]) = item;
- }
+ index = 0; __pyx_t_14 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_14)) goto __pyx_L20_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_14);
+ index = 1; __pyx_t_15 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_15)) goto __pyx_L20_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_15);
+ index = 2; __pyx_t_9 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_9)) goto __pyx_L20_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_9);
+ index = 3; __pyx_t_3 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_3)) goto __pyx_L20_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_3);
+ index = 4; __pyx_t_1 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_1)) goto __pyx_L20_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ index = 5; __pyx_t_2 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_2)) goto __pyx_L20_unpacking_failed;
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if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_16), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_17 = NULL;
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
goto __pyx_L21_unpacking_done;
__pyx_L20_unpacking_failed:;
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- __pyx_t_17 = NULL;
- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
+ if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L21_unpacking_done:;
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@@ -7352,11 +7363,11 @@ static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject
static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_infile = 0;
int __pyx_v_buffer_size;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__buffer_size,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__buffer_size,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -7370,7 +7381,8 @@ static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -7381,6 +7393,10 @@ static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject
if (unlikely(kw_args > 0)) {
if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
+ if (values[1]) {
+ } else {
+ __pyx_v_buffer_size = ((int)65536);
+ }
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
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char *__pyx_v_result;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- char *__pyx_t_1;
+ PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
int __pyx_t_6;
- int __pyx_t_7;
+ PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -7592,8 +7607,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
* r = self.Parser()
*
*/
- __pyx_t_1 = __pyx_v_self->buffer;
- __pyx_v_b = __pyx_t_1;
+ __pyx_v_b = __pyx_v_self->buffer;
/* "pysam/ctabix.pyx":738
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@@ -7602,13 +7616,13 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
* while not feof( self.infile ):
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
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__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 = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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/* "pysam/ctabix.pyx":740
* r = self.Parser()
@@ -7618,8 +7632,8 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
*/
while (1) {
- __pyx_t_4 = (!feof(__pyx_v_self->infile));
- if (!__pyx_t_4) break;
+ __pyx_t_3 = (!feof(__pyx_v_self->infile));
+ if (!__pyx_t_3) break;
/* "pysam/ctabix.pyx":741
*
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* # skip comments
* if (b[0] == '#'): continue
*/
- __pyx_t_4 = (__pyx_v_nbytes == -1);
- if (__pyx_t_4) {
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+ if (__pyx_t_3) {
goto __pyx_L4_break;
goto __pyx_L5;
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*
* # skip empty lines
*/
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- if (__pyx_t_4) {
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goto __pyx_L3_continue;
goto __pyx_L6;
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*
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*/
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- if (!__pyx_t_5) {
- __pyx_t_6 = ((__pyx_v_b[0]) == '\r');
- __pyx_t_7 = __pyx_t_6;
+ __pyx_t_3 = ((__pyx_v_b[0]) == '\x00');
+ if (!__pyx_t_3) {
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+ if (!__pyx_t_4) {
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} else {
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}
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} else {
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}
- if (__pyx_t_5) {
+ if (__pyx_t_4) {
goto __pyx_L3_continue;
goto __pyx_L7;
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- __pyx_t_4 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r');
- __pyx_t_7 = __pyx_t_4;
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} else {
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+ __pyx_t_6 = __pyx_t_4;
}
- if (__pyx_t_7) {
+ if (__pyx_t_6) {
/* "pysam/ctabix.pyx":753
* # make sure that entry is complete
@@ -7716,21 +7730,21 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
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- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
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+ __pyx_t_2 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
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- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
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__Pyx_XDECREF(__pyx_t_2);
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PyObject *__pyx_v_infile = 0;
struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser = 0;
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PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_infile = 0;
PyObject *__pyx_v_parser = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__infile,&__pyx_n_s__parser,0};
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PyObject *__pyx_v_infile = 0;
PyObject *__pyx_v_parser = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0};
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case 0:
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else {
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}
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}
-static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_header(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_header(PyObject *o, void *x) {
return __pyx_pw_5pysam_6ctabix_9Tabixfile_6header_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs(PyObject *o, void *x) {
return __pyx_pw_5pysam_6ctabix_9Tabixfile_7contigs_1__get__(o);
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#endif
};
-static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
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PyErr_Fetch(&etype, &eval, &etb);
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--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_CLEAR(p->parser);
- PyObject_GC_Track(o);
+ Py_XDECREF(((PyObject *)p->parser));
(*Py_TYPE(o)->tp_free)(o);
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struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
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--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_CLEAR(p->parser);
- PyObject_GC_Track(o);
+ Py_XDECREF(((PyObject *)p->parser));
(*Py_TYPE(o)->tp_free)(o);
}
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- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->parser);
- PyObject_GC_Track(o);
+ Py_XDECREF(((PyObject *)p->parser));
(*Py_TYPE(o)->tp_free)(o);
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#endif
/*--- Module creation code ---*/
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- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
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- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
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+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
#endif
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if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
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}
}
- #endif
if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixIterator = &__pyx_type_5pysam_6ctabix_TabixIterator;
if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
@@ -11861,7 +11871,6 @@ PyMODINIT_FUNC PyInit_ctabix(void)
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__;
}
}
- #endif
if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = &__pyx_type_5pysam_6ctabix_TabixHeaderIterator;
if (PyType_Ready(&__pyx_type_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11884,7 +11893,6 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_asVCF = &__pyx_type_5pysam_6ctabix_asVCF;
if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_CPYTHON
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
@@ -11893,7 +11901,6 @@ PyMODINIT_FUNC PyInit_ctabix(void)
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__;
}
}
- #endif
if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = &__pyx_type_5pysam_6ctabix_TabixIteratorParsed;
__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator;
@@ -11919,15 +11926,8 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__pyx_vtabptr_5pysam_10TabProxies_BedProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_10TabProxies_VCFProxy = __Pyx_ImportType("pysam.TabProxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_vtabptr_5pysam_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
- #if CYTHON_COMPILING_IN_PYPY
- sizeof(PyTypeObject),
- #else
- sizeof(PyHeapTypeObject),
- #endif
- 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
@@ -12325,32 +12325,6 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
return result;
}
-static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
- const char* cstring, Py_ssize_t start, Py_ssize_t stop,
- const char* encoding, const char* errors,
- PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
- Py_ssize_t length;
- if (unlikely((start < 0) | (stop < 0))) {
- length = strlen(cstring);
- if (start < 0) {
- start += length;
- if (start < 0)
- start = 0;
- }
- if (stop < 0)
- stop += length;
- }
- length = stop - start;
- if (unlikely(length <= 0))
- return PyUnicode_FromUnicode(NULL, 0);
- cstring += start;
- if (decode_func) {
- return decode_func(cstring, length, errors);
- } else {
- return PyUnicode_Decode(cstring, length, encoding, errors);
- }
-}
-
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
@@ -12386,38 +12360,33 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ if (value == NULL) {
+ value = Py_None;
Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
}
#if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
+ if (!PyClass_Check(type))
#else
- if (PyType_Check(type)) {
+ if (!PyType_Check(type))
#endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
+ {
+ if (value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
+ Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -12450,7 +12419,6 @@ raise_error:
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -12468,36 +12436,12 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
+ } else if (!PyExceptionClass_Check(type)) {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause && cause != Py_None) {
+ if (cause) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -12514,6 +12458,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
+ if (!value) {
+ value = PyObject_CallObject(type, NULL);
+ }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
@@ -12527,7 +12474,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
}
bad:
- Py_XDECREF(owned_instance);
return;
}
#endif
@@ -12541,7 +12487,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
+ PyString_AS_STRING(kw_name));
#endif
}
@@ -12562,72 +12508,48 @@ static int __Pyx_ParseOptionalKeywords(
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
}
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
+ if (*name) {
values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
+ } else {
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
}
}
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -12666,54 +12588,22 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
index, (index == 1) ? "" : "s");
}
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
}
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
@@ -12721,8 +12611,13 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
- } else {
- return __Pyx_IterFinish();
+ } else if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
}
return 0;
}
@@ -12747,9 +12642,12 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
return 0;
}
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
+}
+
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -12758,27 +12656,19 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
*type = local_type;
*value = local_value;
*tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
+ Py_INCREF(local_type);
+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -12786,13 +12676,10 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
+ these objects (XDECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
return 0;
bad:
*type = 0;
@@ -12805,7 +12692,6 @@ bad:
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -12813,12 +12699,8 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -12830,9 +12712,6 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
@@ -12906,6 +12785,7 @@ bad:
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
+ /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -12935,6 +12815,7 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
PyObject *metaclass;
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
+ /* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
@@ -13226,56 +13107,6 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
PyString_AsString(func_name), (void *)op);
#endif
}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
static PyTypeObject __pyx_CyFunctionType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
@@ -13295,7 +13126,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
+ __Pyx_PyCFunction_Call, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -13331,16 +13162,15 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_version_tag*/
#endif
};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
+static int __Pyx_CyFunction_init(void)
+{
if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
return -1;
__pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
+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)
@@ -13349,12 +13179,85 @@ static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t
m->defaults_pyobjects = pyobjects;
return m->defaults;
}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
+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) {
+ return (equals == Py_EQ);
+ } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+ if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyBytes_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
+ else
+ return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
+ } else {
+ int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
+ #if CYTHON_PEP393_ENABLED
+ if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
+ return -1;
+ if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_LENGTH(s1) == 1) {
+ Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
+ Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #else
+ if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_SIZE(s1) == 1) {
+ Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
+ Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #endif
+ } else {
+ int result = PyUnicode_Compare(s1, s2);
+ if ((result == -1) && unlikely(PyErr_Occurred()))
+ return -1;
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -13384,10 +13287,6 @@ 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
@@ -13407,7 +13306,6 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
if (likely(!ret))
return val;
}
- #endif
return (int32_t)-1;
}
}
@@ -13848,23 +13746,6 @@ bad:
return -1;
}
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -13917,6 +13798,23 @@ bad:
}
#endif
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
static void* __Pyx_GetVtable(PyObject *dict) {
void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
diff --git a/pysam/cvcf.c b/pysam/cvcf.c
index 1754ba8..a4eb2db 100644
--- a/pysam/cvcf.c
+++ b/pysam/cvcf.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.4 on Wed Jan 23 22:59:29 2013 */
+/* Generated by Cython 0.16 on Tue Jan 15 06:50:15 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -11,6 +11,7 @@
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
+
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -22,18 +23,22 @@
#define __fastcall
#endif
#endif
+
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
+
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
+
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
+
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
@@ -41,28 +46,28 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
+
+#if CYTHON_COMPILING_IN_PYPY
+ #define __Pyx_PyCFunction_Call PyObject_Call
+#else
+ #define __Pyx_PyCFunction_Call PyCFunction_Call
+#endif
+
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
- #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
- (PyErr_Format(PyExc_TypeError, \
- "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
- (PyObject*)0))
- #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
- !PyComplex_Check(o))
- #define PyIndex_Check __Pyx_PyIndex_Check
+ #define 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"
- #define CYTHON_FORMAT_SSIZE_T "z"
- #define __Pyx_PyIndex_Check PyIndex_Check
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -70,6 +75,7 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
+
typedef struct {
void *buf;
PyObject *obj;
@@ -83,6 +89,7 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
+
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -94,9 +101,11 @@
#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) \
@@ -106,30 +115,31 @@
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
+
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
+
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
+
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+
+
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -137,6 +147,7 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -155,6 +166,7 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
+
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -162,7 +174,9 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
+
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -179,9 +193,11 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
+
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -190,6 +206,7 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
+
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -208,9 +225,11 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
+
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -220,6 +239,7 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
+
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -228,7 +248,6 @@
#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)
@@ -316,11 +335,7 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#else
-#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
-#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
@@ -897,47 +912,42 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
+ if (likely(o != Py_None)) {
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
+ }
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
-#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -953,22 +963,13 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
Py_INCREF(r);
return r;
}
- } else { /* inlined PySequence_GetItem() */
+ }
+ else if (likely(i >= 0)) {
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return NULL;
- i += l;
- }
return m->sq_item(o, i);
}
}
-#else
- if (PySequence_Check(o)) {
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-#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
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static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
-#if CYTHON_COMPILING_IN_PYPY
-#define __Pyx_PyObject_AsDouble(obj) \
-(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
- likely(PyInt_CheckExact(obj)) ? \
- PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
-#else
#define __Pyx_PyObject_AsDouble(obj) \
((likely(PyFloat_CheckExact(obj))) ? \
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
-#endif
static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
+ if (unlikely(d == Py_None)) {
+ __Pyx_RaiseNoneIndexingError();
+ return NULL;
+ }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -1009,48 +1009,28 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
- int result = PySequence_Contains(seq, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+ return unlikely(b < 0) ? b : !b;
+}
+static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
+ return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
+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_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
- int result = PyDict_Contains(dict, item);
- return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
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-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
- PyListObject* L = (PyListObject*) list;
- Py_ssize_t len = Py_SIZE(list);
- if (likely(L->allocated > len)) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
- }
- return PyList_Append(list, x);
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-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
-
static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (unlikely(PyList_Append(L, x) < 0)) return NULL;
+ if (PyList_Append(L, x) < 0) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- } else {
+ }
+ else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
@@ -1060,18 +1040,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
}
}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-
-static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/
-
-static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2,
- int is_tuple, int has_known_size, int decref_tuple);
-
-static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
- Py_ssize_t* p_orig_length, int* p_is_dict);
-static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
- PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
-
#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_SetItemInt_Fast(o, i, v) : \
__Pyx_SetItemInt_Generic(o, to_py_func(i), v))
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return r;
}
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
-#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -1093,26 +1060,13 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje
Py_DECREF(old);
return 1;
}
- } else { /* inlined PySequence_SetItem() */
+ }
+ else if (likely(i >= 0)) {
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_ass_item)) {
- if (unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (unlikely(l < 0)) return -1;
- i += l;
- }
return m->sq_ass_item(o, i, v);
}
}
-#else
-#if CYTHON_COMPILING_IN_PYPY
- if (PySequence_Check(o) && !PyDict_Check(o)) {
-#else
- if (PySequence_Check(o)) {
-#endif
- return PySequence_SetItem(o, i, v);
- }
-#endif
return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
}
@@ -1151,12 +1105,6 @@ static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) {
#endif /* PyAnySet_CheckExact (<= Py2.4) */
#endif /* < Py2.5 */
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
@@ -1213,6 +1161,18 @@ static int __Pyx_CyFunction_init(void);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
+#include <string.h>
+
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
+
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
@@ -1249,30 +1209,22 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
#define __Pyx_Generator_USED
#include <structmember.h>
-#include <frameobject.h>
typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
typedef struct {
PyObject_HEAD
__pyx_generator_body_t body;
PyObject *closure;
+ int is_running;
+ int resume_label;
PyObject *exc_type;
PyObject *exc_value;
PyObject *exc_traceback;
PyObject *gi_weakreflist;
PyObject *classobj;
- PyObject *yieldfrom;
- int resume_label;
- char is_running; // using T_BOOL for property below requires char value
} __pyx_GeneratorObject;
static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
PyObject *closure);
static int __pyx_Generator_init(void);
-static int __Pyx_Generator_clear(PyObject* self);
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
-#else
-#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
-#endif
static int __Pyx_check_binary_version(void);
@@ -1284,10 +1236,10 @@ static int __Pyx_check_binary_version(void);
#endif
#endif
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
@@ -1518,7 +1470,7 @@ 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_135[] = "pysam.cvcf";
static char __pyx_k_138[] = "id numbertype number type description missingvalue";
static char __pyx_k_140[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
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PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_fa = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("get_sequence (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0};
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Py_ssize_t kw_args;
@@ -2422,20 +2375,24 @@ static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObj
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
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- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
+ if (likely(values[2])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa)) != 0)) kw_args--;
+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa);
+ if (likely(values[3])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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@@ -2500,7 +2457,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
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*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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- __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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@@ -2634,7 +2593,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
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+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_regions (wrapper)", 0);
+ __pyx_self = __pyx_self;
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if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
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- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #else
- __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
} else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- #if CYTHON_COMPILING_IN_CPYTHON
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- #else
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- #endif
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
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PyObject *__pyx_v_vcf = 0;
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switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf);
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else goto __pyx_L5_argtuple_error;
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PyObject *__pyx_v_vcf = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
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int __pyx_v_len;
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@@ -8278,7 +8209,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
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if (likely(PyTuple_CheckExact(sequence))) {
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__pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
} else {
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__pyx_t_10 = PyList_GET_ITEM(sequence, 1);
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__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
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- if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
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PyObject *__pyx_v_format = 0;
PyObject *__pyx_v_formatdict = 0;
PyObject *__pyx_v_alt = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,&__pyx_n_s__formatdict,&__pyx_n_s__alt,0};
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__Pyx_RefNannySetupContext("get_expected (wrapper)", 0);
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{
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
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__Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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else {
__Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt);
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else {
__Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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__Pyx_GOTREF(__pyx_t_2);
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+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -8780,7 +8700,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
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__pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
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+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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PyObject *__pyx_v_key = 0;
PyObject *__pyx_v_data = 0;
PyObject *__pyx_v_line = 0;
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PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_add_definition (wrapper)", 0);
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switch (pos_args) {
case 0:
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__Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
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else {
__Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
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+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data);
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__Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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PyObject *__pyx_v_stream = 0;
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PyObject *(*__pyx_t_8)(PyObject *);
Py_ssize_t __pyx_t_9;
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int __pyx_t_11;
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const char *__pyx_filename = NULL;
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else goto __pyx_L5_argtuple_error;
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else {
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PyObject *__pyx_r = NULL;
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- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
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@@ -12664,20 +12528,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
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* else:
@@ -17135,11 +16884,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
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@@ -17148,8 +16897,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
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@@ -17209,11 +16948,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
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PyObject *__pyx_v_stream = 0;
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+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__pos1,&__pyx_n_s__ref1,&__pyx_n_s__alt1,&__pyx_n_s__pos2,&__pyx_n_s__ref2,&__pyx_n_s__alt2,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("compare_calls (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
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Py_ssize_t kw_args;
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
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+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
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else goto __pyx_L5_argtuple_error;
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+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos1);
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__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref1);
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else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
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+ values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt1);
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else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
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+ values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos2);
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__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
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+ values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref2);
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else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 6:
- if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2)) != 0)) kw_args--;
+ values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2);
+ if (likely(values[6])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -22608,7 +22292,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
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+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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@@ -22668,7 +22353,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
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__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -22718,7 +22404,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
* ###########################################################################################################
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__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
@@ -22748,11 +22435,12 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_80connect = {__Pyx_NAMESTR("conn
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PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("connect (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject* values[2] = {0,0};
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Py_ssize_t kw_args;
@@ -22766,10 +22454,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyOb
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
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PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[5] = {0,0,0,0,0};
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@@ -22948,7 +22639,8 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
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if (kw_args > 0) {
@@ -23096,11 +22788,12 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_84validate = {__Pyx_NAMESTR("val
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CYTHON_UNUSED PyObject *__pyx_v_self = 0;
CYTHON_UNUSED PyObject *__pyx_v_record = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("validate (wrapper)", 0);
+ __pyx_self = __pyx_self;
{
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0};
PyObject* values[2] = {0,0};
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Py_ssize_t kw_args;
@@ -23114,10 +22807,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyO
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
+ values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
+ if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record)) != 0)) kw_args--;
+ values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record);
+ if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
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static void __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->vcf);
- PyObject_GC_Track(o);
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+ Py_XDECREF(p->vcf);
+ __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o);
}
static int __pyx_tp_traverse_5pysam_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
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+ if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) {
+ e = __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->vcf) {
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static int __pyx_tp_clear_5pysam_4cvcf_VCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
PyObject* tmp;
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+ if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) {
+ __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o);
+ }
tmp = ((PyObject*)p->vcf);
p->vcf = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
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return r;
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, CYTHON_UNUSED void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(o);
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static void __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->vcffile);
- PyObject_GC_Track(o);
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+ Py_XDECREF(p->vcffile);
+ __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o);
}
static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
- e = ((likely(__pyx_ptype_5pysam_6ctabix_Parser)) ? ((__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) ? __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord)); if (e) return e;
+ if (__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) {
+ e = __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a); if (e) return e;
+ }
if (p->vcffile) {
e = (*v)(p->vcffile, a); if (e) return e;
}
@@ -23481,7 +23178,9 @@ static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v,
static int __pyx_tp_clear_5pysam_4cvcf_asVCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
PyObject* tmp;
- if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) { if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_asVCFRecord);
+ if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) {
+ __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o);
+ }
tmp = ((PyObject*)p->vcffile);
p->vcffile = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -23646,7 +23345,7 @@ static PyTypeObject __pyx_type_5pysam_4cvcf_asVCFRecord = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -23657,9 +23356,7 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyType
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_v_alt);
- PyObject_GC_Track(o);
+ Py_XDECREF(p->__pyx_v_alt);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -23839,7 +23536,7 @@ static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -23852,11 +23549,9 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeOb
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_outer_scope);
- Py_CLEAR(p->__pyx_v_allele);
- Py_CLEAR(p->__pyx_t_0);
- PyObject_GC_Track(o);
+ Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
+ Py_XDECREF(p->__pyx_v_allele);
+ Py_XDECREF(p->__pyx_t_0);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -24048,7 +23743,7 @@ static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -24063,13 +23758,11 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObj
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o;
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->__pyx_v_d);
- Py_CLEAR(p->__pyx_v_line);
- Py_CLEAR(p->__pyx_v_self);
- Py_CLEAR(p->__pyx_v_stream);
- Py_CLEAR(p->__pyx_t_1);
- PyObject_GC_Track(o);
+ Py_XDECREF(p->__pyx_v_d);
+ Py_XDECREF(p->__pyx_v_line);
+ Py_XDECREF(p->__pyx_v_self);
+ Py_XDECREF(p->__pyx_v_stream);
+ Py_XDECREF(p->__pyx_t_1);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -26748,23 +26441,16 @@ PyMODINIT_FUNC PyInit_cvcf(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if PY_MAJOR_VERSION >= 3
- {
- PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!PyDict_GetItemString(modules, "pysam.cvcf")) {
- if (unlikely(PyDict_SetItemString(modules, "pysam.cvcf", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- }
- #endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #if CYTHON_COMPILING_IN_PYPY
- Py_INCREF(__pyx_b);
+ if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
+ #if PY_MAJOR_VERSION < 3
+ Py_INCREF(__pyx_m);
#endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
+ if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -27962,7 +27648,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
+ "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -27976,7 +27662,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
+ PyString_AS_STRING(kw_name));
#endif
}
@@ -27997,72 +27683,48 @@ static int __Pyx_ParseOptionalKeywords(
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- continue;
- }
- name = first_kw_arg;
- #if PY_MAJOR_VERSION < 3
- if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
- while (*name) {
- if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
- && _PyString_Eq(**name, key)) {
- values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- if ((**argname == key) || (
- (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
- && _PyString_Eq(**argname, key))) {
- goto arg_passed_twice;
- }
- argname++;
+ } else {
+ #if PY_MAJOR_VERSION < 3
+ if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
+ #else
+ if (unlikely(!PyUnicode_Check(key))) {
+ #endif
+ goto invalid_keyword_type;
+ } else {
+ for (name = first_kw_arg; *name; name++) {
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) break;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) break;
+ #endif
}
- }
- } else
- #endif
- if (likely(PyUnicode_Check(key))) {
- while (*name) {
- int cmp = (**name == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**name, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) {
+ if (*name) {
values[name-argnames] = value;
- break;
- }
- name++;
- }
- if (*name) continue;
- else {
- PyObject*** argname = argnames;
- while (argname != first_kw_arg) {
- int cmp = (**argname == key) ? 0 :
- #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
- (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
- #endif
- PyUnicode_Compare(**argname, key);
- if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
- if (cmp == 0) goto arg_passed_twice;
- argname++;
+ } else {
+ for (name=argnames; name != first_kw_arg; name++) {
+ if (**name == key) goto arg_passed_twice;
+ #if PY_MAJOR_VERSION >= 3
+ if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
+ PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
+ #else
+ if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
+ _PyString_Eq(**name, key)) goto arg_passed_twice;
+ #endif
+ }
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
}
}
- } else
- goto invalid_keyword_type;
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ __Pyx_RaiseDoubleKeywordsError(function_name, **name);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -28081,9 +27743,10 @@ bad:
return -1;
}
+
+
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -28092,27 +27755,19 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(&local_type, &local_value, &local_tb);
-#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
-#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
-#else
- if (unlikely(PyErr_Occurred()))
-#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- Py_INCREF(local_type);
- Py_INCREF(local_value);
- Py_INCREF(local_tb);
*type = local_type;
*value = local_value;
*tb = local_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
+ Py_INCREF(local_type);
+ Py_INCREF(local_value);
+ Py_INCREF(local_tb);
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -28120,13 +27775,10 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (DECREF may run arbitrary code). */
+ these objects (XDECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(local_type, local_value, local_tb);
-#endif
return 0;
bad:
*type = 0;
@@ -28173,38 +27825,33 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- if (!value || value == Py_None)
- value = NULL;
- else
+ Py_XINCREF(value);
+ Py_XINCREF(tb);
+ if (tb == Py_None) {
+ Py_DECREF(tb);
+ tb = 0;
+ }
+ else if (tb != NULL && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ if (value == NULL) {
+ value = Py_None;
Py_INCREF(value);
- if (!tb || tb == Py_None)
- tb = NULL;
- else {
- Py_INCREF(tb);
- if (!PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
}
#if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
+ if (!PyClass_Check(type))
#else
- if (PyType_Check(type)) {
+ if (!PyType_Check(type))
#endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
- }
-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
- if (value) {
+ {
+ if (value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
+ Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -28237,7 +27884,6 @@ raise_error:
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -28255,36 +27901,12 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *args;
- if (!value)
- args = PyTuple_New(0);
- else if (PyTuple_Check(value)) {
- Py_INCREF(value);
- args = value;
- }
- else
- args = PyTuple_Pack(1, value);
- if (!args)
- goto bad;
- owned_instance = PyEval_CallObject(type, args);
- Py_DECREF(args);
- if (!owned_instance)
- goto bad;
- value = owned_instance;
- if (!PyExceptionInstance_Check(value)) {
- PyErr_Format(PyExc_TypeError,
- "calling %R should have returned an instance of "
- "BaseException, not %R",
- type, Py_TYPE(value));
- goto bad;
- }
- } else {
+ } else if (!PyExceptionClass_Check(type)) {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause && cause != Py_None) {
+ if (cause) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -28301,6 +27923,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
+ if (!value) {
+ value = PyObject_CallObject(type, NULL);
+ }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
@@ -28314,16 +27939,12 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
}
bad:
- Py_XDECREF(owned_instance);
return;
}
#endif
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
-#if CYTHON_COMPILING_IN_PYPY
- float_value = PyNumber_Float(obj);
-#else
if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) {
return PyFloat_AsDouble(obj);
} else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
@@ -28340,7 +27961,6 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyTuple_SET_ITEM(args, 0, 0);
Py_DECREF(args);
}
-#endif
if (likely(float_value)) {
double value = PyFloat_AS_DOUBLE(float_value);
Py_DECREF(float_value);
@@ -28350,53 +27970,23 @@ bad:
return (double)-1;
}
-static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
- PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
-}
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
- PyErr_Format(PyExc_ValueError,
- "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-static CYTHON_INLINE int __Pyx_IterFinish(void) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* exc_type = tstate->curexc_type;
- if (unlikely(exc_type)) {
- if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
- PyObject *exc_value, *exc_tb;
- exc_value = tstate->curexc_value;
- exc_tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
- Py_DECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_tb);
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#else
- if (unlikely(PyErr_Occurred())) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
- }
- return 0;
-#endif
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
+ PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+ index, (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
}
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
@@ -28404,8 +27994,13 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
- } else {
- return __Pyx_IterFinish();
+ } else if (PyErr_Occurred()) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
}
return 0;
}
@@ -28417,197 +28012,13 @@ static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b)
return q;
}
-static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
-}
-
-static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
- if (t == Py_None) {
- __Pyx_RaiseNoneNotIterableError();
- } else if (PyTuple_GET_SIZE(t) < index) {
- __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
- } else {
- __Pyx_RaiseTooManyValuesError(index);
- }
-}
-
-static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
- int is_tuple, int has_known_size, int decref_tuple) {
- Py_ssize_t index;
- PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
- if (!is_tuple && unlikely(!PyTuple_Check(tuple))) {
- iternextfunc iternext;
- iter = PyObject_GetIter(tuple);
- if (unlikely(!iter)) goto bad;
- if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
- iternext = Py_TYPE(iter)->tp_iternext;
- value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
- value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
- if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
- Py_DECREF(iter);
- } else {
- if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) {
- __Pyx_UnpackTupleError(tuple, 2);
- goto bad;
- }
-#if CYTHON_COMPILING_IN_PYPY
- value1 = PySequence_ITEM(tuple, 0);
- if (unlikely(!value1)) goto bad;
- value2 = PySequence_ITEM(tuple, 1);
- if (unlikely(!value2)) goto bad;
-#else
- value1 = PyTuple_GET_ITEM(tuple, 0);
- value2 = PyTuple_GET_ITEM(tuple, 1);
- Py_INCREF(value1);
- Py_INCREF(value2);
-#endif
- if (decref_tuple) { Py_DECREF(tuple); }
- }
- *pvalue1 = value1;
- *pvalue2 = value2;
- return 0;
-unpacking_failed:
- if (!has_known_size && __Pyx_IterFinish() == 0)
- __Pyx_RaiseNeedMoreValuesError(index);
-bad:
- Py_XDECREF(iter);
- Py_XDECREF(value1);
- Py_XDECREF(value2);
- if (decref_tuple) { Py_XDECREF(tuple); }
- return -1;
-}
-static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
- Py_ssize_t* p_orig_length, int* p_source_is_dict) {
- is_dict = is_dict || likely(PyDict_CheckExact(iterable));
- *p_source_is_dict = is_dict;
-#if !CYTHON_COMPILING_IN_PYPY
- if (is_dict) {
- *p_orig_length = PyDict_Size(iterable);
- Py_INCREF(iterable);
- return iterable;
- }
-#endif
- *p_orig_length = 0;
- if (method_name) {
- PyObject* iter;
- iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL);
- if (!iterable)
- return NULL;
-#if !CYTHON_COMPILING_IN_PYPY
- if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
- return iterable;
-#endif
- iter = PyObject_GetIter(iterable);
- Py_DECREF(iterable);
- return iter;
- }
- return PyObject_GetIter(iterable);
-}
-static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos,
- PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
- PyObject* next_item;
-#if !CYTHON_COMPILING_IN_PYPY
- if (source_is_dict) {
- PyObject *key, *value;
- if (unlikely(orig_length != PyDict_Size(iter_obj))) {
- PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
- return -1;
- }
- if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
- return 0;
- }
- if (pitem) {
- PyObject* tuple = PyTuple_New(2);
- if (unlikely(!tuple)) {
- return -1;
- }
- Py_INCREF(key);
- Py_INCREF(value);
- PyTuple_SET_ITEM(tuple, 0, key);
- PyTuple_SET_ITEM(tuple, 1, value);
- *pitem = tuple;
- } else {
- if (pkey) {
- Py_INCREF(key);
- *pkey = key;
- }
- if (pvalue) {
- Py_INCREF(value);
- *pvalue = value;
- }
- }
- return 1;
- } else if (PyTuple_CheckExact(iter_obj)) {
- Py_ssize_t pos = *ppos;
- if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
- *ppos = pos + 1;
- next_item = PyTuple_GET_ITEM(iter_obj, pos);
- Py_INCREF(next_item);
- } else if (PyList_CheckExact(iter_obj)) {
- Py_ssize_t pos = *ppos;
- if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
- *ppos = pos + 1;
- next_item = PyList_GET_ITEM(iter_obj, pos);
- Py_INCREF(next_item);
- } else
-#endif
- {
- next_item = PyIter_Next(iter_obj);
- if (unlikely(!next_item)) {
- return __Pyx_IterFinish();
- }
- }
- if (pitem) {
- *pitem = next_item;
- } else if (pkey && pvalue) {
- if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
- return -1;
- } else if (pkey) {
- *pkey = next_item;
- } else {
- *pvalue = next_item;
- }
- return 1;
-}
static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
}
-static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_dealloc != current_tp_dealloc)
- type = type->tp_base;
- while (type && type->tp_dealloc == current_tp_dealloc)
- type = type->tp_base;
- if (type)
- type->tp_dealloc(obj);
-}
-
-static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_traverse != current_tp_traverse)
- type = type->tp_base;
- while (type && type->tp_traverse == current_tp_traverse)
- type = type->tp_base;
- if (type && type->tp_traverse)
- return type->tp_traverse(obj, v, a);
- return 0;
-}
-
-static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
- PyTypeObject* type = Py_TYPE(obj);
- while (type && type->tp_clear != current_tp_clear)
- type = type->tp_base;
- while (type && type->tp_clear == current_tp_clear)
- type = type->tp_base;
- if (type && type->tp_clear)
- type->tp_clear(obj);
-}
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -28615,12 +28026,8 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
-#else
- PyErr_GetExcInfo(type, value, tb);
-#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -28632,9 +28039,6 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
@@ -28717,6 +28121,7 @@ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
+ /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -28746,6 +28151,7 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
PyObject *metaclass;
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
+ /* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
@@ -29037,56 +28443,6 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
PyString_AsString(func_name), (void *)op);
#endif
}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
static PyTypeObject __pyx_CyFunctionType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
@@ -29106,7 +28462,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
+ __Pyx_PyCFunction_Call, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -29142,16 +28498,15 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_version_tag*/
#endif
};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
+static int __Pyx_CyFunction_init(void)
+{
if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
return -1;
__pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
+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)
@@ -29160,7 +28515,8 @@ static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t
m->defaults_pyobjects = pyobjects;
return m->defaults;
}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
+static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
+{
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults_tuple = tuple;
Py_INCREF(tuple);
@@ -29191,6 +28547,78 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
}
}
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+ if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyBytes_GET_SIZE(s1) == 1) {
+ if (equals == Py_EQ)
+ return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
+ else
+ return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
+ } else {
+ int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
+ #if CYTHON_PEP393_ENABLED
+ if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
+ return -1;
+ if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_LENGTH(s1) == 1) {
+ Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
+ Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #else
+ if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
+ return (equals == Py_NE);
+ } else if (PyUnicode_GET_SIZE(s1) == 1) {
+ Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
+ Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
+ return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
+ #endif
+ } else {
+ int result = PyUnicode_Compare(s1, s2);
+ if ((result == -1) && unlikely(PyErr_Occurred()))
+ return -1;
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+}
+
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
@@ -29593,7 +29021,6 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
@@ -29601,10 +29028,6 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
@@ -29614,70 +29037,9 @@ static PyObject *__Pyx_Generator_Next(PyObject *self);
static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
static PyObject *__Pyx_Generator_Close(PyObject *self);
static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
-static PyTypeObject *__pyx_GeneratorType = 0;
-#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
-#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
-#if 1 || PY_VERSION_HEX < 0x030300B0
-static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
- PyObject *et, *ev, *tb;
- PyObject *value = NULL;
- __Pyx_ErrFetch(&et, &ev, &tb);
- if (!et) {
- Py_XDECREF(tb);
- Py_XDECREF(ev);
- Py_INCREF(Py_None);
- *pvalue = Py_None;
- return 0;
- }
- if (unlikely(et != PyExc_StopIteration) &&
- unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- if (likely(et == PyExc_StopIteration)) {
- if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
- if (!ev) {
- Py_INCREF(Py_None);
- ev = Py_None;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
- *pvalue = ev;
- return 0;
- }
- }
- PyErr_NormalizeException(&et, &ev, &tb);
- if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
- __Pyx_ErrRestore(et, ev, tb);
- return -1;
- }
- Py_XDECREF(tb);
- Py_DECREF(et);
-#if PY_VERSION_HEX >= 0x030300A0
- value = ((PyStopIterationObject *)ev)->value;
- Py_INCREF(value);
- Py_DECREF(ev);
-#else
- {
- PyObject* args = PyObject_GetAttrString(ev, "args");
- Py_DECREF(ev);
- if (likely(args)) {
- value = PyObject_GetItem(args, 0);
- Py_DECREF(args);
- }
- if (unlikely(!value)) {
- __Pyx_ErrRestore(NULL, NULL, NULL);
- Py_INCREF(Py_None);
- value = Py_None;
- }
- }
-#endif
- *pvalue = value;
- return 0;
-}
-#endif
static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
+{
PyObject *exc_type = self->exc_type;
PyObject *exc_value = self->exc_value;
PyObject *exc_traceback = self->exc_traceback;
@@ -29689,18 +29051,14 @@ void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
Py_XDECREF(exc_traceback);
}
static CYTHON_INLINE
-int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
- if (unlikely(gen->is_running)) {
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
+{
+ PyObject *retval;
+ if (unlikely(self->is_running)) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return 1;
+ return NULL;
}
- return 0;
-}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
- PyObject *retval;
- assert(!self->is_running);
if (unlikely(self->resume_label == 0)) {
if (unlikely(value && value != Py_None)) {
PyErr_SetString(PyExc_TypeError,
@@ -29713,240 +29071,81 @@ PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
- if (value) {
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Generators always return to their most recent caller, not
- * necessarily their creator. */
- if (self->exc_traceback) {
- PyThreadState *tstate = PyThreadState_GET();
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_XINCREF(tstate->frame);
- assert(f->f_back == NULL);
- f->f_back = tstate->frame;
- }
-#endif
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
- &self->exc_traceback);
- } else {
+ 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);
-#if CYTHON_COMPILING_IN_PYPY
-#else
- /* Don't keep the reference to f_back any longer than necessary. It
- * may keep a chain of frames alive or it could create a reference
- * cycle. */
- if (self->exc_traceback) {
- PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
- PyFrameObject *f = tb->tb_frame;
- Py_CLEAR(f->f_back);
- }
-#endif
- } else {
+ if (retval)
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
+ else
__Pyx_Generator_ExceptionClear(self);
- }
return retval;
}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
- PyObject *ret;
- PyObject *val = NULL;
- __Pyx_Generator_Undelegate(gen);
- __Pyx_PyGen_FetchStopIterationValue(&val);
- ret = __Pyx_Generator_SendEx(gen, val);
- Py_XDECREF(val);
- return ret;
-}
-static PyObject *__Pyx_Generator_Next(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- ret = Py_TYPE(yf)->tp_iternext(yf);
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, Py_None);
-}
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
- PyObject *yf = gen->yieldfrom;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Send(yf, value);
- } else {
- if (value == Py_None)
- ret = PyIter_Next(yf);
- else
- ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
- }
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, value);
+static PyObject *__Pyx_Generator_Next(PyObject *self)
+{
+ return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
}
-static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
- PyObject *retval = NULL;
- int err = 0;
- if (__Pyx_Generator_CheckExact(yf)) {
- retval = __Pyx_Generator_Close(yf);
- if (!retval)
- return -1;
- } else {
- PyObject *meth;
- gen->is_running = 1;
- meth = PyObject_GetAttrString(yf, "close");
- if (unlikely(!meth)) {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_WriteUnraisable(yf);
- }
- PyErr_Clear();
- } else {
- retval = PyObject_CallFunction(meth, NULL);
- Py_DECREF(meth);
- if (!retval)
- err = -1;
- }
- gen->is_running = 0;
- }
- Py_XDECREF(retval);
- return err;
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
+{
+ return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
}
-static PyObject *__Pyx_Generator_Close(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject *retval, *raised_exception;
- PyObject *yf = gen->yieldfrom;
- int err = 0;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- Py_INCREF(yf);
- err = __Pyx_Generator_CloseIter(gen, yf);
- __Pyx_Generator_Undelegate(gen);
- Py_DECREF(yf);
- }
- if (err == 0)
+static PyObject *__Pyx_Generator_Close(PyObject *self)
+{
+ __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ PyObject *retval;
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(gen, NULL);
+ retval = __Pyx_Generator_SendEx(generator, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
- raised_exception = PyErr_Occurred();
- if (!raised_exception
- || raised_exception == PyExc_StopIteration
-#if PY_VERSION_HEX >= 0x02050000
- || raised_exception == PyExc_GeneratorExit
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
+#if PY_VERSION_HEX < 0x02050000
+ if (PyErr_ExceptionMatches(PyExc_StopIteration))
+#else
+ if (PyErr_ExceptionMatches(PyExc_StopIteration)
+ || PyErr_ExceptionMatches(PyExc_GeneratorExit))
#endif
- || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- if (raised_exception) PyErr_Clear(); /* ignore these errors */
+ PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
+{
+ __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
- PyObject *yf = gen->yieldfrom;
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
- if (unlikely(__Pyx_Generator_CheckRunning(gen)))
- return NULL;
- if (yf) {
- PyObject *ret;
- Py_INCREF(yf);
-#if PY_VERSION_HEX >= 0x02050000
- if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
- int err = __Pyx_Generator_CloseIter(gen, yf);
- Py_DECREF(yf);
- __Pyx_Generator_Undelegate(gen);
- if (err < 0)
- return __Pyx_Generator_SendEx(gen, NULL);
- goto throw_here;
- }
-#endif
- gen->is_running = 1;
- if (__Pyx_Generator_CheckExact(yf)) {
- ret = __Pyx_Generator_Throw(yf, args);
- } else {
- PyObject *meth = PyObject_GetAttrString(yf, "throw");
- if (unlikely(!meth)) {
- Py_DECREF(yf);
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
- gen->is_running = 0;
- return NULL;
- }
- PyErr_Clear();
- __Pyx_Generator_Undelegate(gen);
- gen->is_running = 0;
- goto throw_here;
- }
- ret = PyObject_CallObject(meth, args);
- Py_DECREF(meth);
- }
- gen->is_running = 0;
- Py_DECREF(yf);
- if (!ret) {
- ret = __Pyx_Generator_FinishDelegation(gen);
- }
- return ret;
- }
-throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(gen, NULL);
+ return __Pyx_Generator_SendEx(generator, NULL);
}
-static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
+static int
+__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
+{
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
Py_VISIT(gen->closure);
Py_VISIT(gen->classobj);
- Py_VISIT(gen->yieldfrom);
Py_VISIT(gen->exc_type);
Py_VISIT(gen->exc_value);
Py_VISIT(gen->exc_traceback);
return 0;
}
-static int __Pyx_Generator_clear(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->yieldfrom);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- return 0;
-}
-static void __Pyx_Generator_dealloc(PyObject *self) {
+static void
+__Pyx_Generator_dealloc(PyObject *self)
+{
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject_GC_UnTrack(gen);
if (gen->gi_weakreflist != NULL)
@@ -29958,10 +29157,16 @@ static void __Pyx_Generator_dealloc(PyObject *self) {
return; /* resurrected. :( */
}
PyObject_GC_UnTrack(self);
- __Pyx_Generator_clear(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) {
+static void
+__Pyx_Generator_del(PyObject *self)
+{
PyObject *res;
PyObject *error_type, *error_value, *error_traceback;
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
@@ -29990,13 +29195,11 @@ static void __Pyx_Generator_del(PyObject *self) {
_Py_NewReference(self);
self->ob_refcnt = refcnt;
}
-#if CYTHON_COMPILING_FOR_CPYTHON
assert(PyType_IS_GC(self->ob_type) &&
_Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
/* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
* we need to undo that. */
_Py_DEC_REFTOTAL;
-#endif
/* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
* chain, so no more to do there.
* If COUNT_ALLOCS, the original decref bumped tp_frees, and
@@ -30004,17 +29207,13 @@ static void __Pyx_Generator_del(PyObject *self) {
* undone.
*/
#ifdef COUNT_ALLOCS
- --Py_TYPE(self)->tp_frees;
- --Py_TYPE(self)->tp_allocs;
+ --self->ob_type->tp_frees;
+ --self->ob_type->tp_allocs;
#endif
}
static PyMemberDef __pyx_Generator_memberlist[] = {
{(char *) "gi_running",
-#if PY_VERSION_HEX >= 0x02060000
- T_BOOL,
-#else
- T_BYTE,
-#endif
+ T_INT,
offsetof(__pyx_GeneratorObject, is_running),
READONLY,
NULL},
@@ -30026,7 +29225,7 @@ static PyMethodDef __pyx_Generator_methods[] = {
{__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_GeneratorType_type = {
+static PyTypeObject __pyx_GeneratorType = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("generator"), /*tp_name*/
sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
@@ -30047,7 +29246,7 @@ static PyTypeObject __pyx_GeneratorType_type = {
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
- 0, /*tp_getattro*/
+ PyObject_GenericGetAttr, /*tp_getattro*/
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
@@ -30056,7 +29255,7 @@ static PyTypeObject __pyx_GeneratorType_type = {
0, /*tp_clear*/
0, /*tp_richcompare*/
offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
+ PyObject_SelfIter, /*tp_iter*/
(iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
__pyx_Generator_methods, /*tp_methods*/
__pyx_Generator_memberlist, /*tp_members*/
@@ -30081,10 +29280,12 @@ static PyTypeObject __pyx_GeneratorType_type = {
0, /*tp_version_tag*/
#endif
};
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure) {
+static
+__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure)
+{
__pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
+ PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
if (gen == NULL)
return NULL;
gen->body = body;
@@ -30093,7 +29294,6 @@ static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
gen->is_running = 0;
gen->resume_label = 0;
gen->classobj = NULL;
- gen->yieldfrom = NULL;
gen->exc_type = NULL;
gen->exc_value = NULL;
gen->exc_traceback = NULL;
@@ -30101,14 +29301,9 @@ static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
PyObject_GC_Track(gen);
return gen;
}
-static int __pyx_Generator_init(void) {
- __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
- __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
- if (PyType_Ready(&__pyx_GeneratorType_type)) {
- return -1;
- }
- __pyx_GeneratorType = &__pyx_GeneratorType_type;
- return 0;
+static int __pyx_Generator_init(void)
+{
+ return PyType_Ready(&__pyx_GeneratorType);
}
static int __Pyx_check_binary_version(void) {
@@ -30130,23 +29325,6 @@ static int __Pyx_check_binary_version(void) {
return 0;
}
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -30199,6 +29377,23 @@ bad:
}
#endif
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
static void* __Pyx_GetVtable(PyObject *dict) {
void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
diff --git a/pysam/include/__init__.py b/pysam/include/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pysam/version.py b/pysam/version.py
index eb98027..22b95fa 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,6 +1,6 @@
# pysam versioning information
-__version__ = "0.7.3"
+__version__ = "0.7.4"
__samtools_version__ = "0.1.18"
diff --git a/samtools/__init__.py b/samtools/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/samtools/bcftools/__init__.py b/samtools/bcftools/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/samtools/win32/__init__.py b/samtools/win32/__init__.py
new file mode 100644
index 0000000..e69de29
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 <email at email.com>
+doc_files = README doc/*.html ChangeLog
distribution-name = Red Hat Linux
+packager = TDB <email at email.com>
requires = python
[egg_info]
diff --git a/setup.py b/setup.py
index 182c30f..0cc9c4b 100644
--- a/setup.py
+++ b/setup.py
@@ -137,7 +137,7 @@ except ImportError:
cmdclass = { }
csamtools_sources = [ "pysam/csamtools.c" ]
tabix_sources = [ "pysam/ctabix.c" ]
- tabproxies_sourcess = ["pysam/TabProxies.c" ]
+ tabproxies_sources = ["pysam/TabProxies.c" ]
cvcf_sources = ["pysam/cvcf.c" ]
else:
cmdclass = { 'build_ext' : build_ext }
@@ -228,11 +228,19 @@ metadata = {
'license': "MIT",
'platforms': "ALL",
'url': "http://code.google.com/p/pysam/",
- 'packages' : find_packages(),
+ 'packages' : ['pysam',
+ 'pysam.include',
+ 'pysam.include.samtools',
+ 'pysam.include.samtools.bcftools',
+ 'pysam.include.samtools.win32',
+ 'pysam.include.tabix'],
'requires' : ['cython (>=0.17)'],
'ext_modules': [samtools, tabix, tabproxies, cvcf ],
'cmdclass' : cmdclass,
'install_requires' : ['cython>=0.17',],
+ 'package_dir' : { 'pysam' : 'pysam',
+ 'pysam.include.samtools' : 'samtools',
+ 'pysam.include.tabix' : 'tabix' },
'package_data' : { '' : ['*.pxd', '*.h'], },
# do not pack in order to permit linking to csamtools.so
'zip_safe' :False,
diff --git a/tabix/__init__.py b/tabix/__init__.py
new file mode 100644
index 0000000..e69de29
--
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/pysam.git
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