[med-svn] [pysam] 01/13: Imported Upstream version 0.7.1
Charles Plessy
plessy at alioth.debian.org
Fri Aug 9 09:47:26 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 11d21483ba2333249960e114ca3785d4476ac3d7
Author: Charles Plessy <plessy at debian.org>
Date: Fri Aug 9 18:34:23 2013 +0900
Imported Upstream version 0.7.1
---
MANIFEST.in | 3 +-
PKG-INFO | 2 +-
pysam.egg-info/PKG-INFO | 2 +-
pysam.egg-info/SOURCES.txt | 2 +-
pysam/TabProxies.c | 4 +-
pysam/VCF.py | 1087 -----
pysam/__init__.py | 2 +-
pysam/csamtools.c |10764 ++++++++++++++++----------------------------
pysam/csamtools.pyx | 8 +-
pysam/ctabix.c | 1670 +++----
pysam/ctabix.pyx | 3 +
pysam/cvcf.c | 33 +-
pysam/version.py | 2 +-
setup.cfg | 4 +-
setup.py | 43 +-
tests/example_btag.bam | Bin 0 -> 771 bytes
tests/pysam_test.py | 10 +
17 files changed, 4935 insertions(+), 8704 deletions(-)
diff --git a/MANIFEST.in b/MANIFEST.in
index f613856..0fe44fe 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -21,6 +21,7 @@ include pysam/TabProxies.pxd
include pysam/cvcf.pyx
include pysam/cvcf.pxd
include pysam/cvcf.c
+include pysam/*.c
include pysam/pysam_util.h
include samtools/*.h
include samtools/*/*.h
@@ -44,6 +45,7 @@ include tests/example.py
include tests/pysam_test.py
include tests/segfault_tests.py
include tests/example_*.sam
+include tests/example_btag.bam
include tests/tag_bug.bam
include tests/example.vcf40
include tests/example_empty_header.bam
@@ -56,4 +58,3 @@ include tests/example.gtf.gz.tbi
include tests/example.bed.gz
include tests/example.bed.gz.tbi
include tests/vcf-examples/*.vcf
-
diff --git a/PKG-INFO b/PKG-INFO
index 6e727bf..e0b77b4 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7
+Version: 0.7.1
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO
index 6e727bf..e0b77b4 100644
--- a/pysam.egg-info/PKG-INFO
+++ b/pysam.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7
+Version: 0.7.1
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
diff --git a/pysam.egg-info/SOURCES.txt b/pysam.egg-info/SOURCES.txt
index b59e914..31820bd 100644
--- a/pysam.egg-info/SOURCES.txt
+++ b/pysam.egg-info/SOURCES.txt
@@ -10,7 +10,6 @@ pysam/Pileup.py
pysam/TabProxies.c
pysam/TabProxies.pxd
pysam/TabProxies.pyx
-pysam/VCF.py
pysam/__init__.py
pysam/csamtools.c
pysam/csamtools.pxd
@@ -141,6 +140,7 @@ tests/example.gtf.gz
tests/example.gtf.gz.tbi
tests/example.py
tests/example.vcf40
+tests/example_btag.bam
tests/example_btag.sam
tests/example_empty_header.bam
tests/example_unmapped_reads_no_sq.sam
diff --git a/pysam/TabProxies.c b/pysam/TabProxies.c
index 8c393e0..df3c35e 100644
--- a/pysam/TabProxies.c
+++ b/pysam/TabProxies.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Tue Nov 20 16:56:59 2012 */
+/* Generated by Cython 0.16 on Tue Nov 20 15:06:33 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -970,7 +970,7 @@ static char __pyx_k_54[] = "feature strand.";
static char __pyx_k_55[] = "feature frame.";
static char __pyx_k_56[] = "feature attributes (as a string).";
static char __pyx_k_57[] = "getfilesystemencoding";
-static char __pyx_k_60[] = "/ifs/devel/pysam/pysam/TabProxies.pyx";
+static char __pyx_k_60[] = "/home/andreas/devel/pysam/pysam/TabProxies.pyx";
static char __pyx_k__v[] = "v";
static char __pyx_k__id[] = "id";
static char __pyx_k__alt[] = "alt";
diff --git a/pysam/VCF.py b/pysam/VCF.py
deleted file mode 100644
index 94d63f8..0000000
--- a/pysam/VCF.py
+++ /dev/null
@@ -1,1087 +0,0 @@
-#
-# Code to read, write and edit VCF files
-#
-# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
-# 'chrom': string
-# 'pos': integer
-# 'id': string
-# 'ref': string
-# 'alt': list of strings
-# 'qual': integer
-# 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
-# 'info': dictionary of values (see below)
-# 'format': list of keys (strings)
-# sample keys: dictionary of values (see below)
-#
-# The sample keys are accessible through vcf.getsamples()
-#
-# A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map
-# to a list, containign integers, floats, strings, or characters. Missing values are replaced
-# by a particular value, often -1 or .
-#
-# Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples),
-# the first (and last) the integer representing an allele, and the second the separation character.
-# Note that there is just one genotype per sample, but for consistency the single element is stored in a list.
-#
-# Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible
-# through getheader()
-#
-# The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding
-# 0-based half-open segments. Only variants with a position inside the segment will be parsed. A regions
-# parser is available under parse_regions.
-#
-# When instantiated, a reference can be passed to the VCF class. This may be any class that supports a
-# fetch(chrom, start, end) method.
-#
-#
-#
-# NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file.
-#
-#
-#
-# TODO:
-# only v4.0 writing is complete; alleles are not converted to v3.3 format
-#
-
-from collections import namedtuple, defaultdict
-from operator import itemgetter
-import sys, re, copy, bisect
-
-import pysam
-
-gtsRegEx = re.compile("[|/\\\\]")
-alleleRegEx = re.compile('^[ACGTN]+$')
-
-# Utility function. Uses 0-based coordinates
-def get_sequence(chrom, start, end, fa):
- # obtain sequence from .fa file, without truncation
- if end<=start: return ""
- if not fa: return "N"*(end-start)
- if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
- sequence = fa.fetch(chrom, start, end).upper()
- if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
- return sequence
-
-# Utility function. Parses a region string
-def parse_regions( string ):
- result = []
- for r in string.split(','):
- elts = r.split(':')
- chrom, start, end = elts[0], 0, 3000000000
- if len(elts)==1: pass
- elif len(elts)==2:
- if len(elts[1])>0:
- ielts = elts[1].split('-')
- if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
- try: start, end = int(ielts[0])-1, int(ielts[1])
- except: raise ValueError("Don't understand region string '%s'" % r)
- else:
- raise ValueError("Don't understand region string '%s'" % r)
- result.append( (chrom,start,end) )
- return result
-
-
-FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
-
-###########################################################################################################
-#
-# New class
-#
-###########################################################################################################
-
-class VCFRecord:
- '''vcf record.
-
- initialized from data and vcf meta
- '''
-
- data = None
- vcf = None
-
- def __init__(self, data, vcf):
- self.data, self.vcf = data, vcf
-
- if len(data) != len(self.vcf._samples):
- self.error(str(data),
- self.BAD_NUMBER_OF_COLUMNS,
- "expected %s for %s samples (%s), got %s" % \
- (len(self.vcf._samples),
- len(self.vcf._samples),
- self.vcf._samples,
- len(data)))
-
- property contig:
- def contig( self ): return self.data[0]
-
- property pos:
- def __get__( self ):
- return self.data.pos
-
- property id:
- def __get__( self ): return self.data[2]
-
- property ref:
- def __get__(self ):
- # note: gerton substitutes reference if it can be fixed.
- return self.data[3].upper()
-
- property alt:
- def __get__(self):
- # convert v3.3 to v4.0 alleles below
- alt = self.data[4]
- if alt == ".": alt = []
- else: alt = alt.upper().split(',')
- return alt
-
- property qual:
- def __get__(self):
- qual = self.data[5]
- if qual == ".": qual = -1
- else:
- try: qual = float(qual)
- except: self.error(line,self.QUAL_NOT_NUMERICAL)
-
- property filter:
- def __get__(self):
- # postpone checking that filters exist. Encode missing filter or no filtering as empty list
- if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
- else: filter = cols[6].split(';')
-
- return filter
-
- property info:
- def __get__(self):
- col = self.data[7]
- # dictionary of keys, and list of values
- info = {}
- if col != ".":
- for blurp in col.split(';'):
- elts = blurp.split('=')
- if len(elts) == 1: v = None
- elif len(elts) == 2: v = elts[1]
- else: self.error(str(self.data),self.ERROR_INFO_STRING)
- info[elts[0]] = self.parse_formatdata(elts[0], v, self.vcf._info, line)
- return info
-
- property format:
- def __get__(self):
- return self.data[8].split(':')
-
- def __getitem__(self, key):
-
- # parse sample columns
- values = self.data[self.vcf._sample2column[key]].split(':')
- alt = self.alt
- format = self.format
-
- if len(values) > len(format):
- self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
-
- result = {}
- for idx in range(len(format)):
- expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
- if idx < len(values): value = values[idx]
- else:
- if expected == -1: value = "."
- else: value = ",".join(["."]*expected)
-
- result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, line)
- if expected != -1 and len(result[format[idx]]) != expected:
- self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
- "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
- if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
- result[format[idx]] = result[format[idx]][:expected]
-
- return result
-
- def __str__(self):
- return str(self.data)
-
-class VCF:
-
- # types
- NT_UNKNOWN = 0
- NT_NUMBER = 1
- NT_ALLELES = 2
- NT_NR_ALLELES = 3
- NT_GENOTYPES = 4
- NT_PHASED_GENOTYPES = 5
-
- _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
- 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
- 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
- 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
- 4:"POS_NOT_NUMERICAL:Position column is not numerical",
- 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
- 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
- 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
- 8:"POS_NOT_POSITIVE:Position field must be >0",
- 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
- 10:"ERROR_INFO_STRING:Error while parsing info field",
- 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
- 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
- 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
- 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
- 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
- 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
- 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
- 18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
- 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
- 20:"MISSING_REF:Reference allele missing",
- 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
- 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
- 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
- 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
- 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
- 26:"WRONG_REF:Wrong reference %s",
- 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
- 28:"BAD_CHR_TAG:Error calculating chr tag for %s",
- 29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
- 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"
- }
-
- # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
- _header = []
-
- # version number; 33=v3.3; 40=v4.0
- _version = 40
-
- # info, filter and format data
- _info = {}
- _filter = {}
- _format = {}
-
- # header; and required columns
- _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
- _samples = []
-
- # control behaviour
- _ignored_errors = set([11]) # ERROR_UNKNOWN_KEY
- _warn_errors = set([])
- _leftalign = False
-
- # reference sequence
- _reference = None
-
- # regions to include; None includes everything
- _regions = None
-
- # statefull stuff
- _lineno = -1
- _line = None
- _lines = None
-
- def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
- # make error identifiers accessible by name
- for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
- if _copy != None:
- self._leftalign = _copy._leftalign
- self._header = _copy._header[:]
- self._version = _copy._version
- self._info = copy.deepcopy(_copy._info)
- self._filter = copy.deepcopy(_copy._filter)
- self._format = copy.deepcopy(_copy._format)
- self._samples = _copy._samples[:]
- self._sample2column = copy.deepcopy(_copy._sample2column)
- self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
- self._warn_errors = copy.deepcopy(_copy._warn_errors)
- self._reference = _copy._reference
- self._regions = _copy._regions
- if reference: self._reference = reference
- if regions: self._regions = regions
- if leftalign: self._leftalign = leftalign
- self._lines = lines
-
- def error(self,line,error,opt=None):
- if error in self._ignored_errors: return
- errorlabel, errorstring = self._errors[error].split(':')
- if opt: errorstring = errorstring % opt
- errwarn = ["Error","Warning"][error in self._warn_errors]
- sys.stderr.write("Line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring))
- if error in self._warn_errors: return
- raise ValueError(errorstring)
-
- def parse_format(self,line,format,filter=False):
- if self._version >= 40:
- if not format.startswith('<'):
- self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
- format = "<"+format
- if not format.endswith('>'):
- self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
- format += ">"
- format = format[1:-1]
- data = {'id':None,'number':None,'type':None,'descr':None}
- idx = 0
- while len(format.strip())>0:
- elts = format.strip().split(',')
- first, rest = elts[0], ','.join(elts[1:])
- if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
- if self._version >= 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
- if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- first = ["ID=","Number=","Type=","Description="][idx] + first
- if first.startswith('ID='): data['id'] = first.split('=')[1]
- elif first.startswith('Number='): data['number'] = first.split('=')[1]
- elif first.startswith('Type='): data['type'] = first.split('=')[1]
- elif first.startswith('Description='):
- elts = format.split('"')
- if len(elts)<3:
- self.error(line,self.FORMAT_MISSING_QUOTES)
- elts = first.split('=') + [rest]
- data['descr'] = elts[1]
- rest = '"'.join(elts[2:])
- if rest.startswith(','): rest = rest[1:]
- else:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- format = rest
- idx += 1
- if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
- if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- if not data['descr']:
- self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
- data['descr'] = '<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 f4f1138..7c001d1 100644
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -113,7 +113,7 @@ SAMTOOLS_DISPATCH = {
}
# instantiate samtools commands as python functions
-for key, options in SAMTOOLS_DISPATCH.iteritems():
+for key, options in SAMTOOLS_DISPATCH.items():
cmd, parser = options
globals()[key] = SamtoolsDispatcher(cmd, parser)
diff --git a/pysam/csamtools.c b/pysam/csamtools.c
index b7495db..35b4522 100644
--- a/pysam/csamtools.c
+++ b/pysam/csamtools.c
@@ -1,12 +1,11 @@
-/* Generated by Cython 0.16 on Thu Nov 22 15:20:54 2012 */
+/* Generated by Cython 0.15.1 on Mon Jan 14 23:52:53 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
#else
+
#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
@@ -35,22 +34,10 @@
#define PY_LONG_LONG LONG_LONG
#endif
-#ifndef Py_HUGE_VAL
- #define Py_HUGE_VAL HUGE_VAL
-#endif
-
-#ifdef PYPY_VERSION
-#define CYTHON_COMPILING_IN_PYPY 1
-#define CYTHON_COMPILING_IN_CPYTHON 0
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyCFunction_Call PyObject_Call
-#else
- #define __Pyx_PyCFunction_Call PyCFunction_Call
+#if PY_VERSION_HEX < 0x02040000
+ #define METH_COEXIST 0
+ #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
+ #define PyDict_Contains(d,o) PySequence_Contains(d,o)
#endif
#if PY_VERSION_HEX < 0x02050000
@@ -63,9 +50,6 @@
#define PyNumber_Index(o) PyNumber_Int(o)
#define PyIndex_Check(o) PyNumber_Check(o)
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
- #define __PYX_BUILD_PY_SSIZE_T "i"
-#else
- #define __PYX_BUILD_PY_SSIZE_T "n"
#endif
#if PY_VERSION_HEX < 0x02060000
@@ -99,25 +83,13 @@
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
-#endif
-
-#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
- #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
#if PY_MAJOR_VERSION >= 3
@@ -129,17 +101,6 @@
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
-#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -207,6 +168,15 @@
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -248,14 +218,6 @@
#define __Pyx_DOCSTR(n) (n)
#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
#ifndef __PYX_EXTERN_C
#ifdef __cplusplus
#define __PYX_EXTERN_C extern "C"
@@ -313,7 +275,7 @@
# else
# define CYTHON_UNUSED
# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# elif defined(__ICC) || defined(__INTEL_COMPILER)
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
@@ -338,7 +300,7 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
@@ -370,7 +332,15 @@ static const char *__pyx_f[] = {
"complex.pxd",
};
+static PyObject *__Pyx_Generator_Next(PyObject *self);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
+static PyObject *__Pyx_Generator_Close(PyObject *self);
+static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args, CYTHON_UNUSED PyObject *kwds);
+
+typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
+
/*--- Type declarations ---*/
+struct __pyx_Generator_object;
struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr;
struct __pyx_obj_9csamtools_IteratorRow;
struct __pyx_obj_9csamtools_IteratorRowAllRefs;
@@ -442,8 +412,18 @@ struct __pyx_t_9csamtools_MateData {
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
+struct __pyx_Generator_object {
PyObject_HEAD
+ __pyx_generator_body_t body;
+ int is_running;
+ int resume_label;
+ PyObject *exc_type;
+ PyObject *exc_value;
+ PyObject *exc_traceback;
+};
+
+struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
+ struct __pyx_Generator_object __pyx_base;
PyObject *__pyx_v_x;
PyObject *__pyx_v_y;
PyObject *__pyx_t_0;
@@ -621,7 +601,7 @@ struct __pyx_obj_9csamtools_IteratorRowRegion {
*
*/
struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr {
- PyObject_HEAD
+ struct __pyx_Generator_object __pyx_base;
PyObject *__pyx_v_x;
PyObject *__pyx_v_y;
PyObject *__pyx_t_0;
@@ -844,9 +824,11 @@ struct __pyx_vtabstruct_9csamtools_IteratorRowAll {
int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *);
};
static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;
+
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
+
#if CYTHON_REFNANNY
typedef struct {
void (*INCREF)(void*, PyObject*, int);
@@ -859,21 +841,8 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
#define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
-#ifdef WITH_THREAD
- #define __Pyx_RefNannySetupContext(name, acquire_gil) \
- if (acquire_gil) { \
- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \
- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
- PyGILState_Release(__pyx_gilstate_save); \
- } else { \
- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
- }
-#else
- #define __Pyx_RefNannySetupContext(name, acquire_gil) \
- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
-#endif
- #define __Pyx_RefNannyFinishContext() \
- __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
+ #define __Pyx_RefNannySetupContext(name) __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
+ #define __Pyx_RefNannyFinishContext() __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
#define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
@@ -884,7 +853,7 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo
#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
#define __Pyx_RefNannyDeclarations
- #define __Pyx_RefNannySetupContext(name, acquire_gil)
+ #define __Pyx_RefNannySetupContext(name)
#define __Pyx_RefNannyFinishContext()
#define __Pyx_INCREF(r) Py_INCREF(r)
#define __Pyx_DECREF(r) Py_DECREF(r)
@@ -895,21 +864,23 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
#endif /* CYTHON_REFNANNY */
-#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
-#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
#ifndef CYTHON_PROFILE
#define CYTHON_PROFILE 1
#endif
+
#ifndef CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_PROFILE_REUSE_FRAME 0
#endif
+
#if CYTHON_PROFILE
+
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
+
#if CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_FRAME_MODIFIER static
#define CYTHON_FRAME_DEL
@@ -917,14 +888,17 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
#define CYTHON_FRAME_MODIFIER
#define CYTHON_FRAME_DEL Py_DECREF(__pyx_frame)
#endif
+
#define __Pyx_TraceDeclarations \
static PyCodeObject *__pyx_frame_code = NULL; \
CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \
int __Pyx_use_tracing = 0;
+
#define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \
__Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno); \
}
+
#define __Pyx_TraceException() \
if (unlikely(__Pyx_use_tracing( && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyObject *exc_info = __Pyx_GetExceptionTuple(); \
@@ -934,19 +908,24 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
Py_DECREF(exc_info); \
} \
}
+
#define __Pyx_TraceReturn(result) \
if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyThreadState_GET()->c_profilefunc( \
PyThreadState_GET()->c_profileobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \
CYTHON_FRAME_DEL; \
}
+
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/
static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno); /*proto*/
+
#else
+
#define __Pyx_TraceDeclarations
#define __Pyx_TraceCall(funcname, srcfile, firstlineno)
#define __Pyx_TraceException()
#define __Pyx_TraceReturn(result)
+
#endif /* CYTHON_PROFILE */
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
@@ -963,13 +942,13 @@ static CYTHON_INLINE PyObject* __Pyx_tp_new(PyObject* type_obj) {
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
+ const char* function_name, int kw_allowed); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name, PyObject* kw_name); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name); /*proto*/
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
@@ -979,6 +958,7 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
@@ -986,9 +966,12 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
Py_DECREF(j);
return r;
}
+
+
#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
if (likely(o != Py_None)) {
if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
@@ -1004,9 +987,11 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
+
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
if (likely(o != Py_None)) {
if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
@@ -1022,33 +1007,29 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
+
+
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
- if (PyList_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
+ PyObject *r;
+ if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
}
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
+ else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
}
- else if (likely(i >= 0)) {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- return m->sq_item(o, i);
- }
+ else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
+ r = PySequence_GetItem(o, i);
}
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ else {
+ r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+ }
+ return r;
}
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
@@ -1073,8 +1054,8 @@ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
- return unlikely(b < 0) ? b : !b;
+static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
+ return unlikely(b < 0) ? b : !b;
}
static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
@@ -1114,6 +1095,7 @@ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObjec
Py_INCREF(value);
#else
if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) {
+ /* these presumably have safe hash functions */
value = PyDict_GetItem(d, key);
if (unlikely(!value)) {
value = default_value;
@@ -1124,7 +1106,7 @@ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObjec
m = __Pyx_GetAttrString(d, "get");
if (!m) return NULL;
value = PyObject_CallFunctionObjArgs(m, key,
- (default_value == Py_None) ? NULL : default_value, NULL);
+ (default_value == Py_None) ? NULL : default_value, NULL);
Py_DECREF(m);
}
#endif
@@ -1140,6 +1122,7 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
#define __Pyx_DelItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_DelItemInt_Fast(o, i) : \
__Pyx_DelItem_Generic(o, to_py_func(i)))
+
static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
int r;
if (!j) return -1;
@@ -1147,14 +1130,14 @@ static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
Py_DECREF(j);
return r;
}
+
static CYTHON_INLINE int __Pyx_DelItemInt_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(i >= 0)) {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- return m->sq_ass_item(o, i, (PyObject *)NULL);
- }
+ if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && likely(i >= 0))
+ return PySequence_DelItem(o, i);
+ else {
+ PyObject *j = PyInt_FromSsize_t(i);
+ return __Pyx_DelItem_Generic(o, j);
}
- return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i));
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -1167,47 +1150,19 @@ static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
PyObject *modname); /*proto*/
-#define __Pyx_CyFunction_USED 1
-#include <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 PyTypeObject __pyx_binding_PyCFunctionType_type;
+static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
+
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */
+#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL)
+
+static int __pyx_binding_PyCFunctionType_init(void); /* proto */
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
@@ -1277,25 +1232,6 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-#define __Pyx_Generator_USED
-#include <structmember.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;
-} __pyx_GeneratorObject;
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure);
-static int __pyx_Generator_init(void);
-
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename); /*proto*/
@@ -1303,38 +1239,15 @@ static int __Pyx_check_binary_version(void);
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
-#if !defined(__Pyx_PyIdentifier_FromString)
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
-#else
- #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
-#endif
-#endif
-
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-typedef struct {
- int code_line;
- PyCodeObject* code_object;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename); /*proto*/
+static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
+ int __pyx_lineno, const char *__pyx_filename); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-
/* Module declarations from 'cpython.version' */
/* Module declarations from 'cpython.ref' */
@@ -1429,6 +1342,7 @@ static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
+static PyTypeObject *__pyx_ptype_9csamtools___pyx_Generator = 0;
static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct__genexpr = 0;
static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = 0;
static PyObject *__pyx_v_9csamtools__FILENAME_ENCODING = 0;
@@ -1480,191 +1394,6 @@ static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_chr;
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_UnicodeDecodeError;
-static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile); /* proto */
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static void __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_other); /* proto */
-static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */
-static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self); /* proto */
-static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
-static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self); /* proto */
static char __pyx_k_1[] = "Argument must be string or unicode.";
static char __pyx_k_3[] = "Argument must be string, bytes or unicode.";
static char __pyx_k_5[] = "\t";
@@ -1722,7 +1451,6 @@ static char __pyx_k__H[] = "H";
static char __pyx_k__I[] = "I";
static char __pyx_k__S[] = "S";
static char __pyx_k__Z[] = "Z";
-static char __pyx_k__a[] = "a";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__d[] = "d";
@@ -1854,11 +1582,10 @@ static char __pyx_k_249[] = "getfilesystemencoding";
static char __pyx_k_250[] = "MIDNSHP=X";
static char __pyx_k_251[] = "([MIDNSHP=X])(\\d+)";
static char __pyx_k_253[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_256[] = "/ifs/devel/pysam/pysam/csamtools.pyx";
-static char __pyx_k_257[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
-static char __pyx_k_266[] = "\n stderr is captured.\n ";
-static char __pyx_k_273[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_290[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
+static char __pyx_k_254[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
+static char __pyx_k_255[] = "\n stderr is captured.\n ";
+static char __pyx_k_256[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_262[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
@@ -1877,6 +1604,7 @@ static char __pyx_k__PG[] = "PG";
static char __pyx_k__PI[] = "PI";
static char __pyx_k__PL[] = "PL";
static char __pyx_k__PN[] = "PN";
+static char __pyx_k__PP[] = "PP";
static char __pyx_k__PU[] = "PU";
static char __pyx_k__RG[] = "RG";
static char __pyx_k__SM[] = "SM";
@@ -1900,11 +1628,9 @@ static char __pyx_k__bin[] = "bin";
static char __pyx_k__chr[] = "chr";
static char __pyx_k__dup[] = "dup";
static char __pyx_k__end[] = "end";
-static char __pyx_k__inf[] = "inf";
static char __pyx_k__map[] = "map";
static char __pyx_k__max[] = "max";
static char __pyx_k__min[] = "min";
-static char __pyx_k__ofd[] = "ofd";
static char __pyx_k__ord[] = "ord";
static char __pyx_k__pos[] = "pos";
static char __pyx_k__raw[] = "raw";
@@ -1949,7 +1675,6 @@ static char __pyx_k__warn[] = "warn";
static char __pyx_k___open[] = "_open";
static char __pyx_k__ascii[] = "ascii";
static char __pyx_k__bqual[] = "bqual";
-static char __pyx_k__cargs[] = "cargs";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
static char __pyx_k__flush[] = "flush";
@@ -1987,7 +1712,6 @@ static char __pyx_k__record[] = "record";
static char __pyx_k__region[] = "region";
static char __pyx_k__remove[] = "remove";
static char __pyx_k__reopen[] = "reopen";
-static char __pyx_k__retval[] = "retval";
static char __pyx_k__sorted[] = "sorted";
static char __pyx_k__stderr[] = "stderr";
static char __pyx_k__stdout[] = "stdout";
@@ -2037,10 +1761,6 @@ static char __pyx_k__genotype[] = "genotype";
static char __pyx_k__nextiter[] = "nextiter";
static char __pyx_k__platform[] = "platform";
static char __pyx_k__samtools[] = "samtools";
-static char __pyx_k__stderr_f[] = "stderr_f";
-static char __pyx_k__stderr_h[] = "stderr_h";
-static char __pyx_k__stdout_f[] = "stdout_f";
-static char __pyx_k__stdout_h[] = "stdout_h";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__template[] = "template";
static char __pyx_k__truncate[] = "truncate";
@@ -2068,8 +1788,6 @@ static char __pyx_k__IS_PYTHON3[] = "IS_PYTHON3";
static char __pyx_k__PileupRead[] = "PileupRead";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___buildLine[] = "_buildLine";
-static char __pyx_k__out_stderr[] = "out_stderr";
-static char __pyx_k__out_stdout[] = "out_stdout";
static char __pyx_k__references[] = "references";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__AlignedRead[] = "AlignedRead";
@@ -2082,7 +1800,6 @@ static char __pyx_k__collections[] = "collections";
static char __pyx_k__defaultdict[] = "defaultdict";
static char __pyx_k__nreferences[] = "nreferences";
static char __pyx_k__snp_quality[] = "snp_quality";
-static char __pyx_k__stdout_save[] = "stdout_save";
static char __pyx_k__IndexedReads[] = "IndexedReads";
static char __pyx_k__PileupColumn[] = "PileupColumn";
static char __pyx_k___parseRegion[] = "_parseRegion";
@@ -2175,12 +1892,11 @@ static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_24;
static PyObject *__pyx_n_s_249;
static PyObject *__pyx_kp_s_251;
+static PyObject *__pyx_kp_s_254;
+static PyObject *__pyx_kp_s_255;
static PyObject *__pyx_kp_s_256;
-static PyObject *__pyx_kp_s_257;
-static PyObject *__pyx_kp_s_266;
-static PyObject *__pyx_kp_s_273;
+static PyObject *__pyx_kp_s_262;
static PyObject *__pyx_kp_s_29;
-static PyObject *__pyx_kp_s_290;
static PyObject *__pyx_kp_u_3;
static PyObject *__pyx_kp_s_30;
static PyObject *__pyx_kp_s_31;
@@ -2266,6 +1982,7 @@ static PyObject *__pyx_n_s__PG;
static PyObject *__pyx_n_s__PI;
static PyObject *__pyx_n_s__PL;
static PyObject *__pyx_n_s__PN;
+static PyObject *__pyx_n_s__PP;
static PyObject *__pyx_n_s__PU;
static PyObject *__pyx_n_s__PileupColumn;
static PyObject *__pyx_n_s__PileupProxy;
@@ -2308,7 +2025,6 @@ static PyObject *__pyx_n_s___isOpen;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
static PyObject *__pyx_n_s___samtools_dispatch;
-static PyObject *__pyx_n_s__a;
static PyObject *__pyx_n_s__add_sq_text;
static PyObject *__pyx_n_s__alignment;
static PyObject *__pyx_n_s__all;
@@ -2321,7 +2037,6 @@ static PyObject *__pyx_n_s__bqual;
static PyObject *__pyx_n_s__c;
static PyObject *__pyx_n_s__calcsize;
static PyObject *__pyx_n_s__callback;
-static PyObject *__pyx_n_s__cargs;
static PyObject *__pyx_n_s__catch_stdout;
static PyObject *__pyx_n_s__check_header;
static PyObject *__pyx_n_s__check_sq;
@@ -2365,7 +2080,6 @@ static PyObject *__pyx_n_s__i;
static PyObject *__pyx_n_s__id;
static PyObject *__pyx_n_s__indel;
static PyObject *__pyx_n_s__index;
-static PyObject *__pyx_n_s__inf;
static PyObject *__pyx_n_s__is_del;
static PyObject *__pyx_n_s__is_head;
static PyObject *__pyx_n_s__is_tail;
@@ -2399,13 +2113,10 @@ static PyObject *__pyx_n_s__n_cigar;
static PyObject *__pyx_n_s__nextiter;
static PyObject *__pyx_n_s__nreferences;
static PyObject *__pyx_n_s__object;
-static PyObject *__pyx_n_s__ofd;
static PyObject *__pyx_n_s__offset;
static PyObject *__pyx_n_s__open;
static PyObject *__pyx_n_s__ord;
static PyObject *__pyx_n_s__os;
-static PyObject *__pyx_n_s__out_stderr;
-static PyObject *__pyx_n_s__out_stdout;
static PyObject *__pyx_n_s__pack_into;
static PyObject *__pyx_n_s__path;
static PyObject *__pyx_n_s__pileups;
@@ -2438,7 +2149,6 @@ static PyObject *__pyx_n_s__release;
static PyObject *__pyx_n_s__remove;
static PyObject *__pyx_n_s__reopen;
static PyObject *__pyx_n_s__restore;
-static PyObject *__pyx_n_s__retval;
static PyObject *__pyx_n_s__rlen;
static PyObject *__pyx_n_s__rname;
static PyObject *__pyx_n_s__s;
@@ -2456,12 +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;
@@ -2594,41 +2299,12 @@ 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_262;
-static PyObject *__pyx_k_tuple_264;
-static PyObject *__pyx_k_tuple_267;
-static PyObject *__pyx_k_tuple_269;
-static PyObject *__pyx_k_tuple_271;
-static PyObject *__pyx_k_tuple_274;
-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_281;
-static PyObject *__pyx_k_tuple_282;
-static PyObject *__pyx_k_tuple_284;
-static PyObject *__pyx_k_tuple_286;
-static PyObject *__pyx_k_tuple_288;
-static PyObject *__pyx_k_tuple_291;
-static PyObject *__pyx_k_codeobj_255;
-static PyObject *__pyx_k_codeobj_259;
-static PyObject *__pyx_k_codeobj_261;
-static PyObject *__pyx_k_codeobj_263;
-static PyObject *__pyx_k_codeobj_265;
-static PyObject *__pyx_k_codeobj_268;
-static PyObject *__pyx_k_codeobj_270;
-static PyObject *__pyx_k_codeobj_272;
-static PyObject *__pyx_k_codeobj_280;
-static PyObject *__pyx_k_codeobj_283;
-static PyObject *__pyx_k_codeobj_285;
-static PyObject *__pyx_k_codeobj_287;
-static PyObject *__pyx_k_codeobj_289;
-static PyObject *__pyx_k_codeobj_292;
-static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_k_tuple_261;
+static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
/* "csamtools.pyx":140
* cdef char* CODE2CIGAR= "MIDNSHP=X"
@@ -2638,15 +2314,14 @@ static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_gen
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
+static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_1genexpr[] = "genexpr()";
+static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("genexpr", 0);
+ __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);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
@@ -2654,19 +2329,14 @@ static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self
}
__Pyx_GOTREF(__pyx_cur_scope);
__Pyx_TraceCall("genexpr", __pyx_f[0], 140);
- {
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_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);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = NULL;
- __pyx_L0:;
__Pyx_DECREF(((PyObject *)__pyx_cur_scope));
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
@@ -2674,17 +2344,16 @@ static PyObject *__pyx_pf_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self
return __pyx_r;
}
-static PyObject *__pyx_gb_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_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope = ((struct __pyx_obj_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
- __Pyx_RefNannySetupContext("None", 0);
- switch (__pyx_generator->resume_label) {
+ __Pyx_RefNannySetupContext("None");
+ switch (__pyx_cur_scope->__pyx_base.resume_label) {
case 0: goto __pyx_L3_first_run;
case 1: goto __pyx_L6_resume_from_yield;
default: /* CPython raises the right error here */
@@ -2729,7 +2398,7 @@ static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_gen
__pyx_t_1 = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
@@ -2746,7 +2415,7 @@ static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_gen
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
/* return from generator, yielding value */
- __pyx_generator->resume_label = 1;
+ __pyx_cur_scope->__pyx_base.resume_label = 1;
return __pyx_r;
__pyx_L6_resume_from_yield:;
__pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
@@ -2760,7 +2429,7 @@ static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_gen
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
@@ -2769,11 +2438,11 @@ static PyObject *__pyx_gb_9csamtools_4generator(__pyx_GeneratorObject *__pyx_gen
__Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
- __pyx_generator->resume_label = -1;
+ __pyx_cur_scope->__pyx_base.resume_label = -1;
__Pyx_RefNannyFinishContext();
return NULL;
}
-static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
/* "csamtools.pyx":142
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
@@ -2783,15 +2452,14 @@ static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_ge
*
*/
-static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
+static PyObject *__pyx_pf_9csamtools_3genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_3genexpr[] = "genexpr()";
+static PyObject *__pyx_pf_9csamtools_3genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("genexpr", 0);
+ __Pyx_RefNannySetupContext("genexpr");
__pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
@@ -2799,19 +2467,14 @@ static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self
}
__Pyx_GOTREF(__pyx_cur_scope);
__Pyx_TraceCall("genexpr", __pyx_f[0], 142);
- {
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_9csamtools_7generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __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_4generator1;
+ __Pyx_GIVEREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) __pyx_cur_scope;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = NULL;
- __pyx_L0:;
__Pyx_DECREF(((PyObject *)__pyx_cur_scope));
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
@@ -2819,9 +2482,8 @@ static PyObject *__pyx_pf_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self
return __pyx_r;
}
-static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value) /* generator body */
{
- struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
@@ -2829,8 +2491,8 @@ static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_ge
PyObject *(*__pyx_t_4)(PyObject *);
PyObject *__pyx_t_5 = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("None", 0);
- switch (__pyx_generator->resume_label) {
+ __Pyx_RefNannySetupContext("None");
+ switch (__pyx_cur_scope->__pyx_base.resume_label) {
case 0: goto __pyx_L3_first_run;
case 1: goto __pyx_L6_resume_from_yield;
default: /* CPython raises the right error here */
@@ -2875,7 +2537,7 @@ static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_ge
__pyx_t_1 = __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 = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
@@ -2883,7 +2545,7 @@ static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_ge
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_x);
@@ -2900,7 +2562,7 @@ static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_ge
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
/* return from generator, yielding value */
- __pyx_generator->resume_label = 1;
+ __pyx_cur_scope->__pyx_base.resume_label = 1;
return __pyx_r;
__pyx_L6_resume_from_yield:;
__pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
@@ -2914,7 +2576,7 @@ static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_ge
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
@@ -2924,7 +2586,7 @@ static PyObject *__pyx_gb_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_ge
__Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
- __pyx_generator->resume_label = -1;
+ __pyx_cur_scope->__pyx_base.resume_label = -1;
__Pyx_RefNannyFinishContext();
return NULL;
}
@@ -2946,7 +2608,7 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("from_string_and_size", 0);
+ __Pyx_RefNannySetupContext("from_string_and_size");
__Pyx_TraceCall("from_string_and_size", __pyx_f[0], 24);
/* "csamtools.pyx":25
@@ -3024,7 +2686,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_my_encodeFilename", 0);
+ __Pyx_RefNannySetupContext("_my_encodeFilename");
__Pyx_TraceCall("_my_encodeFilename", __pyx_f[0], 41);
/* "csamtools.pyx":44
@@ -3097,7 +2759,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
__pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
__Pyx_GIVEREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
@@ -3158,7 +2820,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_bytes", 0);
+ __Pyx_RefNannySetupContext("_force_bytes");
__Pyx_TraceCall("_force_bytes", __pyx_f[0], 54);
/* "csamtools.pyx":57
@@ -3308,7 +2970,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_cmdline_bytes", 0);
+ __Pyx_RefNannySetupContext("_force_cmdline_bytes");
__Pyx_TraceCall("_force_cmdline_bytes", __pyx_f[0], 68);
/* "csamtools.pyx":69
@@ -3355,7 +3017,7 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_charptr_to_str", 0);
+ __Pyx_RefNannySetupContext("_charptr_to_str");
__Pyx_TraceCall("_charptr_to_str", __pyx_f[0], 71);
/* "csamtools.pyx":72
@@ -3432,7 +3094,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_str", 0);
+ __Pyx_RefNannySetupContext("_force_str");
__Pyx_TraceCall("_force_str", __pyx_f[0], 77);
/* "csamtools.pyx":79
@@ -3559,7 +3221,7 @@ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makeAlignedRead", 0);
+ __Pyx_RefNannySetupContext("makeAlignedRead");
__Pyx_TraceCall("makeAlignedRead", __pyx_f[0], 160);
/* "csamtools.pyx":162
@@ -3627,7 +3289,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupProxy", 0);
+ __Pyx_RefNannySetupContext("makePileupProxy");
__Pyx_TraceCall("makePileupProxy", __pyx_f[0], 167);
/* "csamtools.pyx":168
@@ -3725,7 +3387,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupRead", 0);
+ __Pyx_RefNannySetupContext("makePileupRead");
__Pyx_TraceCall("makePileupRead", __pyx_f[0], 176);
/* "csamtools.pyx":178
@@ -3850,7 +3512,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
uint8_t __pyx_v_byte_size;
int32_t __pyx_v_nvalues;
PyObject *__pyx_v_values = NULL;
- CYTHON_UNUSED long __pyx_v_x;
+ long __pyx_v_x;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -3863,7 +3525,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("convertBinaryTagToList", 0);
+ __Pyx_RefNannySetupContext("convertBinaryTagToList");
__Pyx_TraceCall("convertBinaryTagToList", __pyx_f[0], 188);
/* "csamtools.pyx":195
@@ -3919,7 +3581,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* for x from 0 <= x < nvalues:
*/
__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;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_values = __pyx_t_1;
__pyx_t_1 = 0;
@@ -3950,6 +3612,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* s += 1
* elif auxtype == 'C':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_int8_t((((int8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -3994,6 +3659,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* s += 1
* elif auxtype == 's':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((((uint8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4038,6 +3706,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* s += 2
* elif auxtype == 'S':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_int16_t((((int16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4082,6 +3753,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* s += 2
* elif auxtype == 'i':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_uint16_t((((uint16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4126,6 +3800,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* s += 4
* elif auxtype == 'I':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_int32_t((((int32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4170,6 +3847,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* s += 4
* elif auxtype == 'f':
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = __Pyx_PyInt_to_py_uint32_t((((uint32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4214,6 +3894,9 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* s += 4
*
*/
+ if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyFloat_FromDouble((((float *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4245,7 +3928,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_5 = __Pyx_PyInt_to_py_int32_t(__pyx_v_nvalues); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
@@ -4293,7 +3976,7 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch_callback", 0);
+ __Pyx_RefNannySetupContext("fetch_callback");
__Pyx_TraceCall("fetch_callback", __pyx_f[0], 239);
/* "csamtools.pyx":244
@@ -4316,7 +3999,7 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
* class PileupColumn(object):
*/
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_a);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_a);
__Pyx_GIVEREF(__pyx_v_a);
@@ -4339,20 +4022,6 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_12PileupColumn_1__str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pw_9csamtools_12PileupColumn_1__str__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12PileupColumn___str__)};
-static PyObject *__pyx_pw_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_12PileupColumn___str__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":260
* list of reads (:class:`pysam.PileupRead`) aligned to this column
* '''
@@ -4361,7 +4030,10 @@ static PyObject *__pyx_pw_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_sel
* "\n" + "\n".join( map(str, self.pileups) )
*/
-static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_12PileupColumn___str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pf_9csamtools_12PileupColumn___str__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12PileupColumn___str__)};
+static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4373,8 +4045,9 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 260);
+ __pyx_self = __pyx_self;
/* "csamtools.pyx":261
* '''
@@ -4409,7 +4082,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje
__pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
@@ -4420,7 +4093,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -4431,7 +4104,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
@@ -4455,7 +4128,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -4466,7 +4139,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObje
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -4521,7 +4194,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_callback", 0);
+ __Pyx_RefNannySetupContext("pileup_callback");
__Pyx_TraceCall("pileup_callback", __pyx_f[0], 264);
/* "csamtools.pyx":281
@@ -4583,7 +4256,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
* cdef int x
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_pileups = __pyx_t_2;
__pyx_t_2 = 0;
@@ -4604,6 +4277,9 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
* p.pileups = pileups
*
*/
+ if (unlikely(((PyObject *)__pyx_v_pileups) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = __pyx_f_9csamtools_makePileupRead((&(__pyx_v_pl[__pyx_v_x]))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_2); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -4627,7 +4303,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
* cdef int pileup_fetch_callback( bam1_t *b, void *data):
*/
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_p);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_p);
__Pyx_GIVEREF(__pyx_v_p);
@@ -4664,7 +4340,7 @@ static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__p
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_fetch_callback", 0);
+ __Pyx_RefNannySetupContext("pileup_fetch_callback");
__Pyx_TraceCall("pileup_fetch_callback", __pyx_f[0], 294);
/* "csamtools.pyx":300
@@ -4702,20 +4378,6 @@ static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__p
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore___init__)};
-static PyObject *__pyx_pw_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_11StderrStore___init__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":308
* stderr is captured.
* '''
@@ -4724,12 +4386,16 @@ static PyObject *__pyx_pw_9csamtools_11StderrStore_1__init__(PyObject *__pyx_sel
* self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore___init__)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 308);
+ __pyx_self = __pyx_self;
/* "csamtools.pyx":309
* '''
@@ -4750,20 +4416,6 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObje
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_2readAndRelease[] = "StderrStore.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_2readAndRelease)};
-static PyObject *__pyx_pw_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_11StderrStore_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":314
* self.stderr_save.setfd( self.stderr_h )
*
@@ -4772,7 +4424,10 @@ static PyObject *__pyx_pw_9csamtools_11StderrStore_3readAndRelease(PyObject *__p
* self.stderr_save.restore()
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_1readAndRelease[] = "StderrStore.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_1readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_1readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_1readAndRelease)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4780,8 +4435,9 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease", 0);
+ __Pyx_RefNannySetupContext("readAndRelease");
__Pyx_TraceCall("readAndRelease", __pyx_f[0], 314);
+ __pyx_self = __pyx_self;
/* "csamtools.pyx":315
*
@@ -4792,7 +4448,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
@@ -4810,20 +4466,6 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_4release[] = "StderrStore.release(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_4release)};
-static PyObject *__pyx_pw_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("release (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_11StderrStore_4release(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":323
* return lines
*
@@ -4832,12 +4474,16 @@ static PyObject *__pyx_pw_9csamtools_11StderrStore_5release(PyObject *__pyx_self
* self.stderr_save.restore()
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_2release[] = "StderrStore.release(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_2release)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release", 0);
+ __Pyx_RefNannySetupContext("release");
__Pyx_TraceCall("release", __pyx_f[0], 323);
+ __pyx_self = __pyx_self;
/* "csamtools.pyx":324
*
@@ -4858,20 +4504,6 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObje
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_6__del__[] = "StderrStore.__del__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_7__del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pw_9csamtools_11StderrStore_7__del__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_6__del__)};
-static PyObject *__pyx_pw_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_11StderrStore_6__del__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":329
* os.remove( self.stderr_f )
*
@@ -4880,7 +4512,10 @@ static PyObject *__pyx_pw_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self
*
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11StderrStore_3__del__[] = "StderrStore.__del__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_3__del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_3__del__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_3__del__)};
+static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4889,8 +4524,9 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObje
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__del__", 0);
+ __Pyx_RefNannySetupContext("__del__");
__Pyx_TraceCall("__del__", __pyx_f[0], 329);
+ __pyx_self = __pyx_self;
/* "csamtools.pyx":330
*
@@ -4920,20 +4556,6 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObje
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_9csamtools_18StderrStoreWindows_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows___init__)};
-static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_18StderrStoreWindows___init__(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":334
* class StderrStoreWindows():
* '''does nothing. stderr can't be redirected on windows'''
@@ -4942,12 +4564,16 @@ static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_1__init__(PyObject *__
* def release(self): pass
*/
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows___init__)};
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 334);
+ __pyx_self = __pyx_self;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -4956,20 +4582,6 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows_2readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_9csamtools_18StderrStoreWindows_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_2readAndRelease)};
-static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":335
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
@@ -4978,7 +4590,10 @@ static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_3readAndRelease(PyObje
*
*/
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows_1readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_1readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_1readAndRelease)};
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4986,11 +4601,12 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease", 0);
+ __Pyx_RefNannySetupContext("readAndRelease");
__Pyx_TraceCall("readAndRelease", __pyx_f[0], 335);
+ __pyx_self = __pyx_self;
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
@@ -5008,20 +4624,6 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows_4release[] = "StderrStoreWindows.release(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_9csamtools_18StderrStoreWindows_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_4release)};
-static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("release (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_18StderrStoreWindows_4release(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":336
* def __init__(self): pass
* def readAndRelease(self): return []
@@ -5030,12 +4632,16 @@ static PyObject *__pyx_pw_9csamtools_18StderrStoreWindows_5release(PyObject *__p
* if platform.system()=='Windows':
*/
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18StderrStoreWindows_2release[] = "StderrStoreWindows.release(self)";
+static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_2release)};
+static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release", 0);
+ __Pyx_RefNannySetupContext("release");
__Pyx_TraceCall("release", __pyx_f[0], 336);
+ __pyx_self = __pyx_self;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -5044,27 +4650,6 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
- __pyx_r = __pyx_pf_9csamtools_9Fastafile___cinit__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
- __Pyx_XDECREF(__pyx_v_args);
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":387
* '''
*
@@ -5073,19 +4658,27 @@ static int __pyx_pw_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyO
* self._filename = NULL
*/
-static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
+static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_RefNannySetupContext("__cinit__");
__Pyx_TraceCall("__cinit__", __pyx_f[0], 387);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
/* "csamtools.pyx":388
*
@@ -5094,7 +4687,7 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_
* self._filename = NULL
* self._open( *args, **kwargs )
*/
- __pyx_v_self->fastafile = NULL;
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
/* "csamtools.pyx":389
* def __cinit__(self, *args, **kwargs ):
@@ -5103,7 +4696,7 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_
* self._open( *args, **kwargs )
*
*/
- __pyx_v_self->_filename = NULL;
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = NULL;
/* "csamtools.pyx":390
* self.fastafile = NULL
@@ -5112,18 +4705,15 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_
*
* def _isOpen( self ):
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_t_3);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_r = 0;
goto __pyx_L0;
@@ -5131,27 +4721,16 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(struct __pyx_obj_9csamtools_
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
__Pyx_AddTraceback("csamtools.Fastafile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_2_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pw_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_9Fastafile_2_isOpen(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":392
* self._open( *args, **kwargs )
*
@@ -5160,7 +4739,9 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self,
* return self.fastafile != NULL
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_1_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5168,7 +4749,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen", 0);
+ __Pyx_RefNannySetupContext("_isOpen");
__Pyx_TraceCall("_isOpen", __pyx_f[0], 392);
/* "csamtools.pyx":394
@@ -5179,7 +4760,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamt
* def __len__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -5198,17 +4779,6 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_9csamt
return __pyx_r;
}
-/* Python wrapper */
-static Py_ssize_t __pyx_pw_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self); /*proto*/
-static Py_ssize_t __pyx_pw_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self) {
- Py_ssize_t __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_9Fastafile_4__len__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":396
* return self.fastafile != NULL
*
@@ -5217,7 +4787,8 @@ static Py_ssize_t __pyx_pw_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self
* raise ValueError( "calling len() on closed file" )
*/
-static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self); /*proto*/
+static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self) {
Py_ssize_t __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -5226,7 +4797,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__len__", 0);
+ __Pyx_RefNannySetupContext("__len__");
__Pyx_TraceCall("__len__", __pyx_f[0], 396);
/* "csamtools.pyx":397
@@ -5236,7 +4807,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam
* raise ValueError( "calling len() on closed file" )
*
*/
- __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":398
@@ -5251,9 +4822,9 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":400
* raise ValueError( "calling len() on closed file" )
@@ -5262,7 +4833,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam
*
* def _open( self,
*/
- __pyx_r = faidx_fetch_nseq(__pyx_v_self->fastafile);
+ __pyx_r = faidx_fetch_nseq(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
goto __pyx_L0;
__pyx_r = 0;
@@ -5277,18 +4848,6 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_4__len__(struct __pyx_obj_9csam
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_6_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
-static PyObject *__pyx_pw_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_open (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_9Fastafile_6_open(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self), ((PyObject *)__pyx_v_filename));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":402
* return faidx_fetch_nseq(self.fastafile)
*
@@ -5297,7 +4856,9 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, P
* '''open an indexed fasta file.
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_3_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
+static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -5308,7 +4869,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open", 0);
+ __Pyx_RefNannySetupContext("_open");
__Pyx_TraceCall("_open", __pyx_f[0], 402);
__Pyx_INCREF(__pyx_v_filename);
@@ -5319,17 +4880,17 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
* if self._filename != NULL: free(self._filename)
* filename = _my_encodeFilename(filename)
*/
- __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
if (__pyx_t_1) {
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":411
* # close a previously opened file
@@ -5338,12 +4899,12 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
* filename = _my_encodeFilename(filename)
* self._filename = strdup(filename)
*/
- __pyx_t_1 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_1) {
- free(__pyx_v_self->_filename);
- goto __pyx_L4;
+ free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":412
* if self.fastafile != NULL: self.close()
@@ -5366,7 +4927,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
*
*/
__pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_filename = strdup(__pyx_t_4);
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = strdup(__pyx_t_4);
/* "csamtools.pyx":414
* filename = _my_encodeFilename(filename)
@@ -5376,7 +4937,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
* if self.fastafile == NULL:
*/
__pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fastafile = fai_load(__pyx_t_4);
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = fai_load(__pyx_t_4);
/* "csamtools.pyx":416
* self.fastafile = fai_load( filename )
@@ -5385,7 +4946,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
* raise IOError("could not open file `%s`" % filename )
*
*/
- __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":417
@@ -5398,7 +4959,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
__pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_3));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
__pyx_t_3 = 0;
@@ -5408,9 +4969,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -5427,18 +4988,6 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6_open(struct __pyx_obj_9csamtoo
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_8close[] = "Fastafile.close(self)";
-static PyObject *__pyx_pw_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("close (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_9Fastafile_8close(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":419
* raise IOError("could not open file `%s`" % filename )
*
@@ -5447,12 +4996,14 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, C
* fai_destroy( self.fastafile )
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_4close[] = "Fastafile.close(self)";
+static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close", 0);
+ __Pyx_RefNannySetupContext("close");
__Pyx_TraceCall("close", __pyx_f[0], 419);
/* "csamtools.pyx":420
@@ -5462,7 +5013,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo
* fai_destroy( self.fastafile )
* self.fastafile = NULL
*/
- __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":421
@@ -5472,7 +5023,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo
* self.fastafile = NULL
*
*/
- fai_destroy(__pyx_v_self->fastafile);
+ fai_destroy(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
/* "csamtools.pyx":422
* if self.fastafile != NULL:
@@ -5481,10 +5032,10 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo
*
* def __dealloc__(self):
*/
- __pyx_v_self->fastafile = NULL;
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -5493,15 +5044,6 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8close(struct __pyx_obj_9csamtoo
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_9Fastafile_10__dealloc__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":424
* self.fastafile = NULL
*
@@ -5510,7 +5052,8 @@ static void __pyx_pw_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self)
* if self._filename != NULL: free(self._filename)
*/
-static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
@@ -5519,7 +5062,7 @@ static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 424);
/* "csamtools.pyx":425
@@ -5529,7 +5072,7 @@ static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamt
* if self._filename != NULL: free(self._filename)
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -5543,12 +5086,12 @@ static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamt
*
* property filename:
*/
- __pyx_t_3 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_3) {
- free(__pyx_v_self->_filename);
- goto __pyx_L3;
+ free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
goto __pyx_L0;
__pyx_L1_error:;
@@ -5560,17 +5103,6 @@ static void __pyx_pf_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_9csamt
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_9Fastafile_8filename___get__(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":430
* property filename:
* '''number of :term:`filename` associated with this object.'''
@@ -5579,7 +5111,8 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_8filename_1__get__(PyObject *__p
* return self._filename
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5590,7 +5123,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 430);
/* "csamtools.pyx":431
@@ -5600,7 +5133,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o
* return self._filename
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -5614,9 +5147,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":432
* def __get__(self):
@@ -5626,7 +5159,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o
* def fetch( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -5646,18 +5179,38 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_12fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n\n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing.\n\n The region is specified by :term:`reference`, *start* and *end*.\n\n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* [...]
-static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":434
+ * return self._filename
+ *
+ * def fetch( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_9Fastafile_6fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n\n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing.\n\n The region is specified by :term:`reference`, *start* and *end*.\n\n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* i [...]
+static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
- PyObject *__pyx_r = 0;
+ int __pyx_v_length;
+ char *__pyx_v_seq;
+ PyObject *__pyx_v_py_seq = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("fetch");
+ __Pyx_TraceCall("fetch", __pyx_f[0], 434);
{
PyObject* values[4] = {0,0,0,0};
@@ -5698,8 +5251,7 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self,
values[3] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
@@ -5708,7 +5260,7 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self,
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -5731,7 +5283,7 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self,
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -5756,36 +5308,6 @@ static PyObject *__pyx_pw_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self,
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_9Fastafile_12fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":434
- * return self._filename
- *
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
- int __pyx_v_length;
- char *__pyx_v_seq;
- PyObject *__pyx_v_py_seq = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch", 0);
- __Pyx_TraceCall("fetch", __pyx_f[0], 434);
__Pyx_INCREF(__pyx_v_start);
__Pyx_INCREF(__pyx_v_end);
__Pyx_INCREF(__pyx_v_region);
@@ -5797,7 +5319,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -5819,9 +5341,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":461
* cdef char * seq
@@ -5848,9 +5370,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L8;
}
- __pyx_L5:;
+ __pyx_L8:;
/* "csamtools.pyx":463
* if not region:
@@ -5864,9 +5386,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_INCREF(__pyx_int_0);
__Pyx_DECREF(__pyx_v_start);
__pyx_v_start = __pyx_int_0;
- goto __pyx_L6;
+ goto __pyx_L9;
}
- __pyx_L6:;
+ __pyx_L9:;
/* "csamtools.pyx":464
* if reference is None: raise ValueError( 'no sequence/region supplied.' )
@@ -5882,9 +5404,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_DECREF(__pyx_v_end);
__pyx_v_end = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
/* "csamtools.pyx":466
* if end is None: end = max_pos -1
@@ -5899,7 +5421,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_start);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_start);
__Pyx_GIVEREF(__pyx_v_start);
@@ -5910,7 +5432,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -5920,9 +5442,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
/* "csamtools.pyx":467
*
@@ -5940,9 +5462,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
__pyx_r = ((PyObject *)__pyx_kp_b_16);
goto __pyx_L0;
- goto __pyx_L9;
+ goto __pyx_L12;
}
- __pyx_L9:;
+ __pyx_L12:;
/* "csamtools.pyx":469
* if start == end: return b""
@@ -5968,7 +5490,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -5978,9 +5500,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ goto __pyx_L13;
}
- __pyx_L10:;
+ __pyx_L13:;
/* "csamtools.pyx":470
* # valid ranges are from 0 to 2^29-1
@@ -6006,7 +5528,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -6016,9 +5538,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ goto __pyx_L14;
}
- __pyx_L11:;
+ __pyx_L14:;
/* "csamtools.pyx":479
* # end-1,
@@ -6030,7 +5552,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__pyx_t_1 = PyNumber_Add(__pyx_v_start, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -6072,9 +5594,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_DECREF(__pyx_v_region);
__pyx_v_region = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L12;
+ goto __pyx_L15;
}
- __pyx_L12:;
+ __pyx_L15:;
/* "csamtools.pyx":483
* region = region.encode('ascii')
@@ -6092,8 +5614,8 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
* else:
* # samtools adds a '\0' at the end
*/
- __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
- goto __pyx_L4;
+ __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
+ goto __pyx_L7;
}
/*else*/ {
@@ -6105,9 +5627,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
* # copy to python
*/
__pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
+ __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
}
- __pyx_L4:;
+ __pyx_L7:;
/* "csamtools.pyx":490
*
@@ -6130,7 +5652,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
__Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
__pyx_r = ((PyObject *)__pyx_kp_b_16);
goto __pyx_L0;
- goto __pyx_L13;
+ goto __pyx_L16;
}
/*else*/ {
@@ -6150,7 +5672,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
* finally:
* free(seq)
*/
- __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L15;}
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L18;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_py_seq = __pyx_t_2;
__pyx_t_2 = 0;
@@ -6168,16 +5690,16 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
PyObject *__pyx_exc_type, *__pyx_exc_value, *__pyx_exc_tb;
int __pyx_exc_lineno;
__pyx_exc_type = 0; __pyx_exc_value = 0; __pyx_exc_tb = 0; __pyx_exc_lineno = 0;
- __pyx_why = 0; goto __pyx_L16;
- __pyx_L15: {
+ __pyx_why = 0; goto __pyx_L19;
+ __pyx_L18: {
__pyx_why = 4;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_ErrFetch(&__pyx_exc_type, &__pyx_exc_value, &__pyx_exc_tb);
__pyx_exc_lineno = __pyx_lineno;
- goto __pyx_L16;
+ goto __pyx_L19;
}
- __pyx_L16:;
+ __pyx_L19:;
free(__pyx_v_seq);
switch (__pyx_why) {
case 4: {
@@ -6191,7 +5713,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_12fetch(struct __pyx_obj_9csamto
}
}
}
- __pyx_L13:;
+ __pyx_L16:;
/* "csamtools.pyx":498
* free(seq)
@@ -6235,7 +5757,7 @@ static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fa
char *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_fetch", 0);
+ __Pyx_RefNannySetupContext("_fetch");
__Pyx_TraceCall("_fetch", __pyx_f[0], 500);
/* "csamtools.pyx":507
@@ -6263,13 +5785,13 @@ static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fa
* '''
*/
-static int __pyx_f_9csamtools_count_callback(CYTHON_UNUSED bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
int *__pyx_v_counter;
int __pyx_r;
__Pyx_RefNannyDeclarations
long __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count_callback", 0);
+ __Pyx_RefNannySetupContext("count_callback");
__Pyx_TraceCall("count_callback", __pyx_f[0], 512);
/* "csamtools.pyx":515
@@ -6313,7 +5835,7 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p
int __pyx_t_2;
int __pyx_t_3;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate_callback", 0);
+ __Pyx_RefNannySetupContext("mate_callback");
__Pyx_TraceCall("mate_callback", __pyx_f[0], 526);
/* "csamtools.pyx":529
@@ -6380,27 +5902,6 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
- __pyx_r = __pyx_pf_9csamtools_7Samfile___cinit__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
- __Pyx_XDECREF(__pyx_v_args);
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":592
* '''
*
@@ -6409,19 +5910,27 @@ static int __pyx_pw_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObj
* self._filename = NULL
*/
-static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
+static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_RefNannySetupContext("__cinit__");
__Pyx_TraceCall("__cinit__", __pyx_f[0], 592);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
/* "csamtools.pyx":593
*
@@ -6430,7 +5939,7 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Sa
* self._filename = NULL
* self.isbam = False
*/
- __pyx_v_self->samfile = NULL;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
/* "csamtools.pyx":594
* def __cinit__(self, *args, **kwargs ):
@@ -6439,7 +5948,7 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Sa
* self.isbam = False
* self.isstream = False
*/
- __pyx_v_self->_filename = NULL;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = NULL;
/* "csamtools.pyx":595
* self.samfile = NULL
@@ -6448,7 +5957,7 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Sa
* self.isstream = False
* self._open( *args, **kwargs )
*/
- __pyx_v_self->isbam = 0;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = 0;
/* "csamtools.pyx":596
* self._filename = NULL
@@ -6457,7 +5966,7 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Sa
* self._open( *args, **kwargs )
*
*/
- __pyx_v_self->isstream = 0;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream = 0;
/* "csamtools.pyx":597
* self.isbam = False
@@ -6466,18 +5975,15 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Sa
*
* # allocate memory for iterator
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_t_3);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "csamtools.pyx":600
*
@@ -6486,7 +5992,7 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Sa
*
* def _isOpen( self ):
*/
- __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
__pyx_r = 0;
goto __pyx_L0;
@@ -6494,27 +6000,16 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(struct __pyx_obj_9csamtools_Sa
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_4);
__Pyx_AddTraceback("csamtools.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_2_isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pw_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_2_isOpen(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":602
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
@@ -6523,7 +6018,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, C
* return self.samfile != NULL
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_1_isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -6531,7 +6028,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtoo
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen", 0);
+ __Pyx_RefNannySetupContext("_isOpen");
__Pyx_TraceCall("_isOpen", __pyx_f[0], 602);
/* "csamtools.pyx":604
@@ -6542,7 +6039,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtoo
* def _hasIndex( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -6561,18 +6058,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_9csamtoo
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_4_hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
-static PyObject *__pyx_pw_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_hasIndex (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_4_hasIndex(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":606
* return self.samfile != NULL
*
@@ -6581,7 +6066,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self,
* return self.index != NULL
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_2_hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -6589,7 +6076,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_hasIndex", 0);
+ __Pyx_RefNannySetupContext("_hasIndex");
__Pyx_TraceCall("_hasIndex", __pyx_f[0], 606);
/* "csamtools.pyx":608
@@ -6600,7 +6087,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamt
* def _open( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -6619,10 +6106,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_9csamt
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_6_open[] = "Samfile._open(self, filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True, check_header=True, check_sq=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
-static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":610
+ * return self.index != NULL
+ *
+ * def _open( self, # <<<<<<<<<<<<<<
+ * filename,
+ * mode = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_3_open[] = "Samfile._open(self, filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True, check_header=True, check_sq=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_filename = 0;
PyObject *__pyx_v_mode = 0;
struct __pyx_obj_9csamtools_Samfile *__pyx_v_template = 0;
@@ -6634,10 +6128,45 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyO
PyObject *__pyx_v_add_sq_text = 0;
PyObject *__pyx_v_check_header = 0;
PyObject *__pyx_v_check_sq = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,&__pyx_n_s__check_header,&__pyx_n_s__check_sq,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_msg = NULL;
+ bam_header_t *__pyx_v_header_to_write;
+ PyObject *__pyx_v_bmode = 0;
+ char *__pyx_v_ctext;
+ PyObject *__pyx_v_n = NULL;
+ PyObject *__pyx_v_x = NULL;
+ PyObject *__pyx_v_name = NULL;
+ PyObject *__pyx_v_store = NULL;
+ PyObject *__pyx_v_ref = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_open (wrapper)", 0);
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_t_11;
+ char *__pyx_t_12;
+ Py_ssize_t __pyx_t_13;
+ Py_ssize_t __pyx_t_14;
+ PyObject *(*__pyx_t_15)(PyObject *);
+ size_t __pyx_t_16;
+ int32_t __pyx_t_17;
+ long __pyx_t_18;
+ uint32_t __pyx_t_19;
+ const char* __pyx_t_20;
+ int __pyx_t_21;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,&__pyx_n_s__check_header,&__pyx_n_s__check_sq,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_open");
+ __Pyx_TraceCall("_open", __pyx_f[0], 610);
{
PyObject* values[11] = {0,0,0,0,0,0,0,0,0,0,0};
@@ -6708,8 +6237,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyO
values[10] = __pyx_k_23;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 11: values[10] = PyTuple_GET_ITEM(__pyx_args, 10);
case 10: values[9] = PyTuple_GET_ITEM(__pyx_args, 9);
case 9: values[8] = PyTuple_GET_ITEM(__pyx_args, 8);
@@ -6725,7 +6253,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyO
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
if (likely(values[0])) kw_args--;
@@ -6782,7 +6310,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyO
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -6821,66 +6349,10 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyO
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_7Samfile_6_open(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_template, __pyx_v_referencenames, __pyx_v_referencelengths, __pyx_v_text, __pyx_v_header, __pyx_v_port, __pyx_v_add_sq_text, __pyx_v_check_header, __pyx_v_check_sq);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":610
- * return self.index != NULL
- *
- * def _open( self, # <<<<<<<<<<<<<<
- * filename,
- * mode = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq) {
- CYTHON_UNUSED PyObject *__pyx_v_msg = NULL;
- bam_header_t *__pyx_v_header_to_write;
- PyObject *__pyx_v_bmode = 0;
- char *__pyx_v_ctext;
- PyObject *__pyx_v_n = NULL;
- PyObject *__pyx_v_x = NULL;
- PyObject *__pyx_v_name = NULL;
- PyObject *__pyx_v_store = NULL;
- PyObject *__pyx_v_ref = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- int __pyx_t_9;
- int __pyx_t_10;
- int __pyx_t_11;
- char *__pyx_t_12;
- Py_ssize_t __pyx_t_13;
- Py_ssize_t __pyx_t_14;
- PyObject *(*__pyx_t_15)(PyObject *);
- size_t __pyx_t_16;
- int32_t __pyx_t_17;
- long __pyx_t_18;
- uint32_t __pyx_t_19;
- const char* __pyx_t_20;
- int __pyx_t_21;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open", 0);
- __Pyx_TraceCall("_open", __pyx_f[0], 610);
__Pyx_INCREF(__pyx_v_filename);
__Pyx_INCREF(__pyx_v_referencenames);
__Pyx_INCREF(__pyx_v_text);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":630
*
@@ -6913,19 +6385,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* referencenames=referencenames,
* referencelengths=referencelengths,
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
/* "csamtools.pyx":633
* try:
@@ -6934,7 +6406,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* referencelengths=referencelengths,
* text=text, header=header, port=port,
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
/* "csamtools.pyx":634
* self._open(filename, 'rb', template=template,
@@ -6943,7 +6415,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* text=text, header=header, port=port,
* check_header=check_header,
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
/* "csamtools.pyx":635
* referencenames=referencenames,
@@ -6952,9 +6424,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* check_header=check_header,
* check_sq=check_sq)
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
/* "csamtools.pyx":636
* referencelengths=referencelengths,
@@ -6963,7 +6435,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* check_sq=check_sq)
* return
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
/* "csamtools.pyx":637
* text=text, header=header, port=port,
@@ -6972,8 +6444,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* return
* except ValueError, msg:
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __pyx_t_8 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
@@ -6989,19 +6461,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*/
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L8_try_return;
+ goto __pyx_L11_try_return;
}
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L11_try_end;
- __pyx_L8_try_return:;
+ goto __pyx_L14_try_end;
+ __pyx_L11_try_return:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
goto __pyx_L0;
- __pyx_L4_error:;
+ __pyx_L7_error:;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
@@ -7017,7 +6489,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_9 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_9) {
__Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_6);
@@ -7026,20 +6498,20 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L5_exception_handled;
+ goto __pyx_L8_exception_handled;
}
- __pyx_L6_except_error:;
+ __pyx_L9_except_error:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
goto __pyx_L1_error;
- __pyx_L5_exception_handled:;
+ __pyx_L8_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
- __pyx_L11_try_end:;
+ __pyx_L14_try_end:;
}
/* "csamtools.pyx":642
@@ -7049,10 +6521,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* referencenames=referencenames,
* referencelengths=referencelengths,
*/
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
@@ -7109,7 +6581,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
@@ -7126,9 +6598,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":650
* return
@@ -7194,17 +6666,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* self.samfile = NULL
*
*/
- __pyx_t_1 = (__pyx_v_self->samfile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
if (__pyx_t_1) {
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L14;
+ goto __pyx_L17;
}
- __pyx_L14:;
+ __pyx_L17:;
/* "csamtools.pyx":656
* # close a previously opened file
@@ -7213,7 +6685,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*
* cdef bam_header_t * header_to_write
*/
- __pyx_v_self->samfile = NULL;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
/* "csamtools.pyx":659
*
@@ -7231,12 +6703,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* filename = _my_encodeFilename(filename)
* cdef bytes bmode = mode.encode('ascii')
*/
- __pyx_t_1 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_1) {
- free(__pyx_v_self->_filename);
- goto __pyx_L15;
+ free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
+ goto __pyx_L18;
}
- __pyx_L15:;
+ __pyx_L18:;
/* "csamtools.pyx":662
*
@@ -7275,7 +6747,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_filename = strdup(__pyx_t_12);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = strdup(__pyx_t_12);
/* "csamtools.pyx":667
* #cfilename = filename.encode(_FILENAME_ENCODING)
@@ -7285,7 +6757,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* self.isbam = len(mode) > 1 and mode[1] == 'b'
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0);
/* "csamtools.pyx":669
* self.isstream = strcmp( filename, "-" ) == 0
@@ -7305,7 +6777,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
} else {
__pyx_t_11 = __pyx_t_1;
}
- __pyx_v_self->isbam = __pyx_t_11;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = __pyx_t_11;
/* "csamtools.pyx":671
* self.isbam = len(mode) > 1 and mode[1] == 'b'
@@ -7339,7 +6811,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* strncmp(filename,"ftp:",4) == 0
*
*/
- __pyx_v_self->isremote = __pyx_t_10;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote = __pyx_t_10;
/* "csamtools.pyx":675
*
@@ -7381,7 +6853,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* elif header:
*/
__pyx_v_header_to_write = __pyx_v_template->samfile->header;
- goto __pyx_L17;
+ goto __pyx_L20;
}
/* "csamtools.pyx":685
@@ -7401,8 +6873,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*
* else:
*/
- __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->_buildHeader(__pyx_v_self, __pyx_v_header);
- goto __pyx_L17;
+ __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->_buildHeader(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_header);
+ goto __pyx_L20;
}
/*else*/ {
@@ -7451,7 +6923,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* header_to_write.n_targets = len(referencenames)
*/
__pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
__pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_14 = 0;
__pyx_t_15 = NULL;
@@ -7461,10 +6933,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
+ if (PyList_CheckExact(__pyx_t_8)) {
if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_8)) break;
__pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
+ } else if (PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
__pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
} else {
@@ -7537,10 +7009,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_15 = Py_TYPE(__pyx_t_5)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_5)) {
+ if (PyList_CheckExact(__pyx_t_5)) {
if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break;
__pyx_t_8 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_5)) {
+ } else if (PyTuple_CheckExact(__pyx_t_5)) {
if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
__pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
} else {
@@ -7693,7 +7165,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
*/
__pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
__Pyx_DECREF(__pyx_v_text);
__pyx_v_text = ((PyObject *)__pyx_t_5);
__pyx_t_5 = 0;
@@ -7725,7 +7197,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_7 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
@@ -7765,7 +7237,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_text);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_text);
__Pyx_GIVEREF(__pyx_v_text);
@@ -7776,9 +7248,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_DECREF(__pyx_v_text);
__pyx_v_text = __pyx_t_5;
__pyx_t_5 = 0;
- goto __pyx_L24;
+ goto __pyx_L27;
}
- __pyx_L24:;
+ __pyx_L27:;
/* "csamtools.pyx":715
* text = ''.join(text)
@@ -7842,9 +7314,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* header_to_write.hash = NULL
*/
memcpy(__pyx_v_header_to_write->text, __pyx_v_ctext, strlen(__pyx_v_ctext));
- goto __pyx_L27;
+ goto __pyx_L30;
}
- __pyx_L27:;
+ __pyx_L30:;
/* "csamtools.pyx":723
* memcpy( header_to_write.text, ctext, strlen(ctext) )
@@ -7864,7 +7336,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*/
__pyx_v_header_to_write->rg2lib = NULL;
}
- __pyx_L17:;
+ __pyx_L20:;
/* "csamtools.pyx":728
* # open file. Header gets written to file at the same time for bam files
@@ -7890,7 +7362,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*/
__pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->samfile = samopen(__pyx_t_20, __pyx_t_12, __pyx_v_header_to_write);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, __pyx_v_header_to_write);
/* "csamtools.pyx":730
* store = StderrStore()
@@ -7931,10 +7403,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* elif mode[0] == "r":
*/
bam_header_destroy(__pyx_v_header_to_write);
- goto __pyx_L28;
+ goto __pyx_L31;
}
- __pyx_L28:;
- goto __pyx_L16;
+ __pyx_L31:;
+ goto __pyx_L19;
}
/* "csamtools.pyx":736
@@ -7968,7 +7440,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* not os.path.exists( filename ):
* raise IOError( "file `%s` not found" % filename)
*/
- __pyx_t_1 = (!__pyx_v_self->isremote);
+ __pyx_t_1 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
if (__pyx_t_1) {
/* "csamtools.pyx":740
@@ -7987,7 +7459,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
@@ -8018,7 +7490,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_32), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -8028,9 +7500,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L29;
+ goto __pyx_L32;
}
- __pyx_L29:;
+ __pyx_L32:;
/* "csamtools.pyx":744
*
@@ -8041,7 +7513,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*/
__pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->samfile = samopen(__pyx_t_20, __pyx_t_12, NULL);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, NULL);
/* "csamtools.pyx":745
* # try to detect errors
@@ -8050,7 +7522,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
*
*/
- __pyx_t_1 = (__pyx_v_self->samfile == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":746
@@ -8063,7 +7535,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_33), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -8073,9 +7545,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L30;
+ goto __pyx_L33;
}
- __pyx_L30:;
+ __pyx_L33:;
/* "csamtools.pyx":749
*
@@ -8084,7 +7556,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* if self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
/* "csamtools.pyx":750
* # bam files require a valid header
@@ -8093,7 +7565,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
* else:
*/
- __pyx_t_1 = (__pyx_v_self->samfile->header == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":751
@@ -8106,7 +7578,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -8116,10 +7588,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L32;
+ goto __pyx_L35;
}
- __pyx_L32:;
- goto __pyx_L31;
+ __pyx_L35:;
+ goto __pyx_L34;
}
/*else*/ {
@@ -8132,7 +7604,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_t_10 = (__pyx_v_self->samfile->header == NULL);
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
__pyx_t_11 = __pyx_t_10;
} else {
__pyx_t_11 = __pyx_t_1;
@@ -8149,7 +7621,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_35), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -8159,11 +7631,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L33;
+ goto __pyx_L36;
}
- __pyx_L33:;
+ __pyx_L36:;
}
- __pyx_L31:;
+ __pyx_L34:;
/* "csamtools.pyx":759
* # disabled for autodetection to work
@@ -8174,7 +7646,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*/
__pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- __pyx_t_1 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
__pyx_t_10 = __pyx_t_1;
} else {
__pyx_t_10 = __pyx_t_11;
@@ -8191,7 +7663,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -8201,12 +7673,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L34;
+ goto __pyx_L37;
}
- __pyx_L34:;
- goto __pyx_L16;
+ __pyx_L37:;
+ goto __pyx_L19;
}
- __pyx_L16:;
+ __pyx_L19:;
/* "csamtools.pyx":762
* raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
@@ -8215,7 +7687,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* raise IOError("could not open file `%s`" % filename )
*
*/
- __pyx_t_10 = (__pyx_v_self->samfile == NULL);
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
if (__pyx_t_10) {
/* "csamtools.pyx":763
@@ -8228,7 +7700,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -8238,9 +7710,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L35;
+ goto __pyx_L38;
}
- __pyx_L35:;
+ __pyx_L38:;
/* "csamtools.pyx":766
*
@@ -8254,7 +7726,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_10) {
- __pyx_t_11 = __pyx_v_self->isbam;
+ __pyx_t_11 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam;
} else {
__pyx_t_11 = __pyx_t_10;
}
@@ -8267,7 +7739,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* if not os.path.exists(filename + b".bai"):
* self.index = NULL
*/
- __pyx_t_11 = (!__pyx_v_self->isremote);
+ __pyx_t_11 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
if (__pyx_t_11) {
/* "csamtools.pyx":769
@@ -8288,7 +7760,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_7 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
@@ -8308,8 +7780,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* else:
* # returns NULL if there is no index or index could not be opened
*/
- __pyx_v_self->index = NULL;
- goto __pyx_L38;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = NULL;
+ goto __pyx_L41;
}
/*else*/ {
@@ -8321,7 +7793,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* raise IOError("error while opening index `%s` " % filename )
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->index = bam_index_load(__pyx_t_12);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12);
/* "csamtools.pyx":774
* # returns NULL if there is no index or index could not be opened
@@ -8330,7 +7802,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* raise IOError("error while opening index `%s` " % filename )
* else:
*/
- __pyx_t_10 = (__pyx_v_self->index == NULL);
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
if (__pyx_t_10) {
/* "csamtools.pyx":775
@@ -8343,7 +7815,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
@@ -8353,12 +7825,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L39;
+ goto __pyx_L42;
}
- __pyx_L39:;
+ __pyx_L42:;
}
- __pyx_L38:;
- goto __pyx_L37;
+ __pyx_L41:;
+ goto __pyx_L40;
}
/*else*/ {
@@ -8370,7 +7842,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* raise IOError("error while opening index `%s` " % filename )
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->index = bam_index_load(__pyx_t_12);
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12);
/* "csamtools.pyx":778
* else:
@@ -8379,7 +7851,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* raise IOError("error while opening index `%s` " % filename )
*
*/
- __pyx_t_10 = (__pyx_v_self->index == NULL);
+ __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
if (__pyx_t_10) {
/* "csamtools.pyx":779
@@ -8392,7 +7864,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
@@ -8402,11 +7874,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L40;
+ goto __pyx_L43;
}
- __pyx_L40:;
+ __pyx_L43:;
}
- __pyx_L37:;
+ __pyx_L40:;
/* "csamtools.pyx":781
* raise IOError("error while opening index `%s` " % filename )
@@ -8415,7 +7887,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
* self.start_offset = bam_tell( self.samfile.x.bam )
*
*/
- __pyx_t_10 = (!__pyx_v_self->isstream);
+ __pyx_t_10 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream);
if (__pyx_t_10) {
/* "csamtools.pyx":782
@@ -8425,13 +7897,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
*
* def gettid( self, reference ):
*/
- __pyx_v_self->start_offset = bam_tell(__pyx_v_self->samfile->x.bam);
- goto __pyx_L41;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset = bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam);
+ goto __pyx_L44;
}
- __pyx_L41:;
- goto __pyx_L36;
+ __pyx_L44:;
+ goto __pyx_L39;
}
- __pyx_L36:;
+ __pyx_L39:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -8459,18 +7931,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_open(struct __pyx_obj_9csamtools
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_8gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
-static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("gettid (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_8gettid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_reference));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":784
* self.start_offset = bam_tell( self.samfile.x.bam )
*
@@ -8479,7 +7939,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, Py
* convert :term:`reference` name into numerical :term:`tid`
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_4gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -8491,7 +7953,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("gettid", 0);
+ __Pyx_RefNannySetupContext("gettid");
__Pyx_TraceCall("gettid", __pyx_f[0], 784);
__Pyx_INCREF(__pyx_v_reference);
@@ -8502,7 +7964,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool
* reference = _force_bytes(reference)
* return pysam_reference2tid( self.samfile.header, reference )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -8516,9 +7978,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":791
* '''
@@ -8542,7 +8004,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_5 = PyBytes_AsString(__pyx_v_reference); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(__pyx_v_self->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -8563,18 +8025,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8gettid(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_10getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
-static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("getrname (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_10getrname(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":794
* return pysam_reference2tid( self.samfile.header, reference )
*
@@ -8583,7 +8033,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self,
* convert numerical :term:`tid` into :term:`reference` name.'''
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_5getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -8595,7 +8047,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getrname", 0);
+ __Pyx_RefNannySetupContext("getrname");
__Pyx_TraceCall("getrname", __pyx_f[0], 794);
/* "csamtools.pyx":797
@@ -8605,7 +8057,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -8619,9 +8071,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":798
* convert numerical :term:`tid` into :term:`reference` name.'''
@@ -8634,7 +8086,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
__Pyx_GOTREF(__pyx_t_2);
if (__Pyx_PyObject_IsTrue(__pyx_t_2)) {
__Pyx_DECREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_1, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -8652,10 +8104,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
* return _charptr_to_str(self.samfile.header.target_name[tid])
*
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_tid);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_tid);
__Pyx_GIVEREF(__pyx_v_tid);
@@ -8666,7 +8118,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__pyx_t_2 = 0;
@@ -8676,9 +8128,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":800
* if not 0 <= tid < self.samfile.header.n_targets:
@@ -8689,7 +8141,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10getrname(struct __pyx_obj_9csamt
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_tid); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -8729,7 +8181,7 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_getrname", 0);
+ __Pyx_RefNannySetupContext("_getrname");
__Pyx_TraceCall("_getrname", __pyx_f[0], 802);
/* "csamtools.pyx":805
@@ -8783,7 +8235,7 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
__pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
@@ -8794,7 +8246,7 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -8832,18 +8284,47 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_12_parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
-static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":810
+ * return self.samfile.header.target_name[tid]
+ *
+ * def _parseRegion( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_6_parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ PY_LONG_LONG __pyx_v_rstart;
+ PY_LONG_LONG __pyx_v_rend;
+ PyObject *__pyx_v_parts = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_parseRegion (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PY_LONG_LONG __pyx_t_6;
+ int __pyx_t_7;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_parseRegion");
+ __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810);
{
PyObject* values[4] = {0,0,0,0};
@@ -8884,8 +8365,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_s
values[3] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
@@ -8894,7 +8374,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_s
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -8917,7 +8397,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_s
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -8942,45 +8422,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_s
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_7Samfile_12_parseRegion(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":810
- * return self.samfile.header.target_name[tid]
- *
- * def _parseRegion( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
- int __pyx_v_rtid;
- PY_LONG_LONG __pyx_v_rstart;
- PY_LONG_LONG __pyx_v_rend;
- PyObject *__pyx_v_parts = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PY_LONG_LONG __pyx_t_6;
- int __pyx_t_7;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- Py_ssize_t __pyx_t_12;
- int __pyx_t_13;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_parseRegion", 0);
- __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810);
__Pyx_INCREF(__pyx_v_reference);
__Pyx_INCREF(__pyx_v_region);
@@ -9045,14 +8486,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
* except OverflowError:
* raise ValueError( 'start out of range (%i)' % start )
*/
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
__pyx_v_rstart = __pyx_t_6;
}
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
- goto __pyx_L11_try_end;
- __pyx_L4_error:;
+ goto __pyx_L14_try_end;
+ __pyx_L7_error:;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "csamtools.pyx":839
@@ -9065,7 +8506,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
if (__pyx_t_7) {
__Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_9);
@@ -9077,40 +8518,40 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
*
* if end != None:
*/
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_11));
PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
__Pyx_Raise(__pyx_t_10, 0, 0, 0);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L5_exception_handled;
+ goto __pyx_L8_exception_handled;
}
- __pyx_L6_except_error:;
+ __pyx_L9_except_error:;
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
goto __pyx_L1_error;
- __pyx_L5_exception_handled:;
+ __pyx_L8_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
- __pyx_L11_try_end:;
+ __pyx_L14_try_end:;
}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":842
* raise ValueError( 'start out of range (%i)' % start )
@@ -9146,14 +8587,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
* except OverflowError:
* raise ValueError( 'end out of range (%i)' % end )
*/
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L18_error;}
__pyx_v_rend = __pyx_t_6;
}
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L22_try_end;
- __pyx_L15_error:;
+ goto __pyx_L25_try_end;
+ __pyx_L18_error:;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -9170,7 +8611,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
if (__pyx_t_7) {
__Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_1);
@@ -9182,40 +8623,40 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
*
* if region:
*/
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_11));
PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
__Pyx_Raise(__pyx_t_10, 0, 0, 0);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L16_exception_handled;
+ goto __pyx_L19_exception_handled;
}
- __pyx_L17_except_error:;
+ __pyx_L20_except_error:;
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
goto __pyx_L1_error;
- __pyx_L16_exception_handled:;
+ __pyx_L19_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
- __pyx_L22_try_end:;
+ __pyx_L25_try_end:;
}
- goto __pyx_L14;
+ goto __pyx_L17;
}
- __pyx_L14:;
+ __pyx_L17:;
/* "csamtools.pyx":848
* raise ValueError( 'end out of range (%i)' % end )
@@ -9253,7 +8694,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_43));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_43));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
@@ -9293,7 +8734,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
@@ -9306,9 +8747,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rstart = __pyx_t_6;
- goto __pyx_L26;
+ goto __pyx_L29;
}
- __pyx_L26:;
+ __pyx_L29:;
/* "csamtools.pyx":853
* reference = parts[0]
@@ -9323,7 +8764,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_1 = __Pyx_GetItemInt(__pyx_v_parts, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -9333,12 +8774,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rend = __pyx_t_6;
- goto __pyx_L27;
+ goto __pyx_L30;
}
- __pyx_L27:;
- goto __pyx_L25;
+ __pyx_L30:;
+ goto __pyx_L28;
}
- __pyx_L25:;
+ __pyx_L28:;
/* "csamtools.pyx":855
* if len(parts) >= 3: rend = int(parts[2])
@@ -9354,9 +8795,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_INCREF(((PyObject *)__pyx_k_tuple_44));
__pyx_r = ((PyObject *)__pyx_k_tuple_44);
goto __pyx_L0;
- goto __pyx_L28;
+ goto __pyx_L31;
}
- __pyx_L28:;
+ __pyx_L31:;
/* "csamtools.pyx":857
* if not reference: return 0, 0, 0, 0
@@ -9365,10 +8806,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -9392,7 +8833,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), __pyx_v_reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -9402,9 +8843,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L29;
+ goto __pyx_L32;
}
- __pyx_L29:;
+ __pyx_L32:;
/* "csamtools.pyx":859
* rtid = self.gettid( reference )
@@ -9420,7 +8861,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_9 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_9);
@@ -9431,7 +8872,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
@@ -9441,9 +8882,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_Raise(__pyx_t_9, 0, 0, 0);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L30;
+ goto __pyx_L33;
}
- __pyx_L30:;
+ __pyx_L33:;
/* "csamtools.pyx":860
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
@@ -9464,7 +8905,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -9474,9 +8915,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L31;
+ goto __pyx_L34;
}
- __pyx_L31:;
+ __pyx_L34:;
/* "csamtools.pyx":861
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
@@ -9497,7 +8938,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
@@ -9507,9 +8948,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__Pyx_Raise(__pyx_t_9, 0, 0, 0);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L32;
+ goto __pyx_L35;
}
- __pyx_L32:;
+ __pyx_L35:;
/* "csamtools.pyx":863
* if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
@@ -9526,7 +8967,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
__pyx_t_8 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
__Pyx_INCREF(__pyx_int_1);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_int_1);
__Pyx_GIVEREF(__pyx_int_1);
@@ -9563,18 +9004,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_14reset[] = "Samfile.reset(self)\nreset file position to beginning of read section.";
-static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("reset (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_14reset(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":865
* return 1, rtid, rstart, rend
*
@@ -9583,7 +9012,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CY
* return self.seek( self.start_offset, 0 )
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_7reset[] = "Samfile.reset(self)\nreset file position to beginning of read section.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -9593,7 +9024,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtool
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_RefNannySetupContext("reset");
__Pyx_TraceCall("reset", __pyx_f[0], 865);
/* "csamtools.pyx":867
@@ -9604,12 +9035,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtool
* def seek( self, uint64_t offset, int where = 0):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(__pyx_v_self->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_int_0);
@@ -9639,29 +9070,44 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14reset(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_16seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
-static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":869
+ * return self.seek( self.start_offset, 0 )
+ *
+ * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
+ * '''
+ * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_8seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
uint64_t __pyx_v_offset;
int __pyx_v_where;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("seek (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("seek");
+ __Pyx_TraceCall("seek", __pyx_f[0], 869);
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset);
if (likely(values[0])) kw_args--;
@@ -9673,11 +9119,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyO
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- if (values[1]) {
- } else {
- __pyx_v_where = ((int)0);
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -9702,32 +9144,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyO
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_7Samfile_16seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_offset, __pyx_v_where);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":869
- * return self.seek( self.start_offset, 0 )
- *
- * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
- * '''
- * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("seek", 0);
- __Pyx_TraceCall("seek", __pyx_f[0], 869);
/* "csamtools.pyx":874
* '''
@@ -9736,7 +9152,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -9758,9 +9174,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":876
* if not self._isOpen():
@@ -9769,7 +9185,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
/* "csamtools.pyx":877
@@ -9784,9 +9200,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
+ __pyx_L7:;
/* "csamtools.pyx":878
* if not self.isbam:
@@ -9795,7 +9211,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
* raise OSError("seek no available in streams")
*
*/
- if (__pyx_v_self->isstream) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) {
/* "csamtools.pyx":879
* raise NotImplementedError("seek only available in bam files")
@@ -9809,9 +9225,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L8;
}
- __pyx_L5:;
+ __pyx_L8:;
/* "csamtools.pyx":881
* raise OSError("seek no available in streams")
@@ -9821,7 +9237,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
* def tell( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(__pyx_v_self->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -9841,18 +9257,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16seek(struct __pyx_obj_9csamtools
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_18tell[] = "Samfile.tell(self)\n\n return current file position\n ";
-static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("tell (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_18tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":883
* return bam_seek( self.samfile.x.bam, offset, where )
*
@@ -9861,7 +9265,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYT
* return current file position
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_9tell[] = "Samfile.tell(self)\n\n return current file position\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -9872,7 +9278,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("tell", 0);
+ __Pyx_RefNannySetupContext("tell");
__Pyx_TraceCall("tell", __pyx_f[0], 883);
/* "csamtools.pyx":887
@@ -9882,7 +9288,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -9904,9 +9310,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":889
* if not self._isOpen():
@@ -9915,7 +9321,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools
* raise NotImplementedError("seek only available in bam files")
*
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
/* "csamtools.pyx":890
@@ -9930,9 +9336,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":892
* raise NotImplementedError("seek only available in bam files")
@@ -9942,7 +9348,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools
* def fetch( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(__pyx_v_self->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -9962,20 +9368,52 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18tell(struct __pyx_obj_9csamtools
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_20fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n [...]
-static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":894
+ * return bam_tell( self.samfile.x.bam )
+ *
+ * def fetch( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_10fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n [...]
+static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_callback = 0;
PyObject *__pyx_v_until_eof = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ int __pyx_v_reopen;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_t_15;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("fetch");
+ __Pyx_TraceCall("fetch", __pyx_f[0], 894);
{
PyObject* values[6] = {0,0,0,0,0,0};
@@ -10026,8 +9464,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py
values[5] = __pyx_k_54;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
@@ -10038,7 +9475,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -10071,7 +9508,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -10100,48 +9537,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, Py
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_7Samfile_20fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_until_eof);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":894
- * return bam_tell( self.samfile.x.bam )
- *
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof) {
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- int __pyx_v_reopen;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_t_14;
- int __pyx_t_15;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch", 0);
- __Pyx_TraceCall("fetch", __pyx_f[0], 894);
/* "csamtools.pyx":924
* cdef int rtid, rstart, rend, has_coord
@@ -10150,7 +9545,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -10172,9 +9567,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":927
* raise ValueError( "I/O operation on closed file" )
@@ -10183,10 +9578,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
*
* if self.isstream: reopen = False
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -10237,23 +9632,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed;
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed;
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_6);
- index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed;
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L5_unpacking_done;
- __pyx_L4_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L5_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -10275,9 +9670,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
* else: reopen = True
*
*/
- if (__pyx_v_self->isstream) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) {
__pyx_v_reopen = 0;
- goto __pyx_L6;
+ goto __pyx_L9;
}
/*else*/ {
@@ -10290,7 +9685,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
*/
__pyx_v_reopen = 1;
}
- __pyx_L6:;
+ __pyx_L9:;
/* "csamtools.pyx":932
* else: reopen = True
@@ -10299,7 +9694,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" )
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
/* "csamtools.pyx":933
*
@@ -10311,7 +9706,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
@@ -10320,7 +9715,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_14 = (!__pyx_t_4);
if (__pyx_t_14) {
- __pyx_t_4 = (!__pyx_v_self->isremote);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
__pyx_t_15 = __pyx_t_4;
} else {
__pyx_t_15 = __pyx_t_14;
@@ -10343,9 +9738,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
/* "csamtools.pyx":936
* raise ValueError( "fetch called on bamfile without index" )
@@ -10371,9 +9766,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ goto __pyx_L13;
}
- __pyx_L10:;
+ __pyx_L13:;
/* "csamtools.pyx":938
* if callback:
@@ -10382,7 +9777,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
* return bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
@@ -10396,9 +9791,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ goto __pyx_L14;
}
- __pyx_L11:;
+ __pyx_L14:;
/* "csamtools.pyx":939
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
@@ -10416,12 +9811,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
* else:
* if has_coord:
*/
- __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_r = __pyx_t_5;
__pyx_t_5 = 0;
goto __pyx_L0;
- goto __pyx_L9;
+ goto __pyx_L12;
}
/*else*/ {
@@ -10449,10 +9844,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_7);
@@ -10468,14 +9863,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_GOTREF(__pyx_t_7);
if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_r = __pyx_t_7;
__pyx_t_7 = 0;
goto __pyx_L0;
- goto __pyx_L12;
+ goto __pyx_L15;
}
/*else*/ {
@@ -10498,24 +9893,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
__pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L13;
+ goto __pyx_L16;
}
/*else*/ {
@@ -10528,10 +9923,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
__pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAllRefs)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -10539,12 +9934,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__pyx_t_6 = 0;
goto __pyx_L0;
}
- __pyx_L13:;
+ __pyx_L16:;
}
- __pyx_L12:;
+ __pyx_L15:;
}
- __pyx_L9:;
- goto __pyx_L7;
+ __pyx_L12:;
+ goto __pyx_L10;
}
/*else*/ {
@@ -10569,9 +9964,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ goto __pyx_L17;
}
- __pyx_L14:;
+ __pyx_L17:;
/* "csamtools.pyx":959
* raise ValueError ("fetching by region is not available for sam files" )
@@ -10595,9 +9990,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L15;
+ goto __pyx_L18;
}
- __pyx_L15:;
+ __pyx_L18:;
/* "csamtools.pyx":962
* raise NotImplementedError( "callback not implemented yet" )
@@ -10606,7 +10001,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
* raise ValueError( "fetch called for samfile without header")
*
*/
- __pyx_t_3 = (__pyx_v_self->samfile->header == NULL);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
if (__pyx_t_3) {
/* "csamtools.pyx":963
@@ -10621,9 +10016,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ goto __pyx_L19;
}
- __pyx_L16:;
+ __pyx_L19:;
/* "csamtools.pyx":967
* # check if targets are defined
@@ -10632,7 +10027,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
* warnings.warn( "fetch called for samfile without header")
*
*/
- __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
if (__pyx_t_3) {
/* "csamtools.pyx":968
@@ -10651,9 +10046,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L17;
+ goto __pyx_L20;
}
- __pyx_L17:;
+ __pyx_L20:;
/* "csamtools.pyx":970
* warnings.warn( "fetch called for samfile without header")
@@ -10664,17 +10059,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -10682,7 +10077,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
__pyx_t_7 = 0;
goto __pyx_L0;
}
- __pyx_L7:;
+ __pyx_L10:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -10702,23 +10097,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20fetch(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_22mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
-static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("mate (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_7Samfile_22mate(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":972
* return IteratorRowAll( self, reopen=reopen )
*
@@ -10727,7 +10105,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyO
* '''return the mate of :class:`AlignedRead` *read*.
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_11mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
uint32_t __pyx_v_flag;
__pyx_t_9csamtools_MateData __pyx_v_mate_data;
int __pyx_v_x;
@@ -10741,8 +10121,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate", 0);
+ __Pyx_RefNannySetupContext("mate");
__Pyx_TraceCall("mate", __pyx_f[0], 972);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":985
*
@@ -10751,7 +10132,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
*
* if flag & BAM_FPAIRED == 0:
*/
- __pyx_v_flag = __pyx_v_read->_delegate->core.flag;
+ __pyx_v_flag = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.flag;
/* "csamtools.pyx":987
* cdef uint32_t flag = read._delegate.core.flag
@@ -10770,13 +10151,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
* if flag & BAM_FMUNMAP != 0:
* raise ValueError( "mate %s: is unmapped" % (read.qname))
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_69), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
__pyx_t_3 = 0;
@@ -10786,9 +10167,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":989
* if flag & BAM_FPAIRED == 0:
@@ -10807,13 +10188,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
*
* cdef MateData mate_data
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_70), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__pyx_t_2 = 0;
@@ -10823,9 +10204,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":994
* cdef MateData mate_data
@@ -10834,7 +10215,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
* mate_data.mate = NULL
* # xor flags to get the other mate
*/
- __pyx_v_mate_data.name = ((char *)bam1_qname(__pyx_v_read->_delegate));
+ __pyx_v_mate_data.name = ((char *)bam1_qname(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate));
/* "csamtools.pyx":995
*
@@ -10870,7 +10251,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
*
* if mate_data.mate == NULL:
*/
- bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback);
+ bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mtid, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos, (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback);
/* "csamtools.pyx":1008
* mate_callback )
@@ -10894,9 +10275,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
/* "csamtools.pyx":1011
* raise ValueError( "mate not found" )
@@ -10947,19 +10328,49 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_22mate(struct __pyx_obj_9csamtools
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_24count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n\n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not [...]
-static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1015
+ * return dest
+ *
+ * def count( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_12count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n\n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not [...]
+static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_until_eof = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_counter;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("count (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("count");
+ __Pyx_TraceCall("count", __pyx_f[0], 1015);
{
PyObject* values[5] = {0,0,0,0,0};
@@ -11001,8 +10412,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py
values[4] = __pyx_k_73;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -11012,7 +10422,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -11040,7 +10450,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -11067,46 +10477,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, Py
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_7Samfile_24count(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_until_eof);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1015
- * return dest
- *
- * def count( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof) {
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_counter;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_t_14;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count", 0);
- __Pyx_TraceCall("count", __pyx_f[0], 1015);
__Pyx_INCREF(__pyx_v_region);
/* "csamtools.pyx":1033
@@ -11116,7 +10486,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -11138,9 +10508,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1036
* raise ValueError( "I/O operation on closed file" )
@@ -11149,10 +10519,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
*
* cdef int counter
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -11203,23 +10573,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed;
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed;
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_6);
- index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed;
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L5_unpacking_done;
- __pyx_L4_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L5_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -11250,7 +10620,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" )
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
/* "csamtools.pyx":1042
*
@@ -11262,7 +10632,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
@@ -11271,7 +10641,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_13 = (!__pyx_t_4);
if (__pyx_t_13) {
- __pyx_t_4 = (!__pyx_v_self->isremote);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
__pyx_t_14 = __pyx_t_4;
} else {
__pyx_t_14 = __pyx_t_13;
@@ -11294,9 +10664,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
/* "csamtools.pyx":1045
* raise ValueError( "fetch called on bamfile without index" )
@@ -11321,9 +10691,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
/* "csamtools.pyx":1047
* if not region:
@@ -11332,7 +10702,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
* bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
@@ -11346,9 +10716,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
+ goto __pyx_L12;
}
- __pyx_L9:;
+ __pyx_L12:;
/* "csamtools.pyx":1054
* rend,
@@ -11357,7 +10727,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
* return counter
* else:
*/
- bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback);
+ bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback);
/* "csamtools.pyx":1055
* <void*>&counter,
@@ -11372,7 +10742,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__pyx_r = __pyx_t_5;
__pyx_t_5 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L9;
}
/*else*/ {
@@ -11389,7 +10759,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L6:;
+ __pyx_L9:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -11410,20 +10780,50 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_24count(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_26pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n [...]
-static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1059
+ * raise ValueError ("count for a region is not available for sam files" )
+ *
+ * def pileup( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_13pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n [...]
+static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_callback = 0;
PyObject *__pyx_v_kwargs = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
- PyObject *__pyx_r = 0;
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ bam_plbuf_t *__pyx_v_buf;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("pileup (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("pileup");
+ __Pyx_TraceCall("pileup", __pyx_f[0], 1059);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL;
__Pyx_GOTREF(__pyx_v_kwargs);
{
@@ -11475,8 +10875,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P
values[4] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -11486,7 +10885,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -11514,7 +10913,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -11542,47 +10941,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, P
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_7Samfile_26pileup(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_kwargs);
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1059
- * raise ValueError ("count for a region is not available for sam files" )
- *
- * def pileup( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs) {
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- bam_plbuf_t *__pyx_v_buf;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup", 0);
- __Pyx_TraceCall("pileup", __pyx_f[0], 1059);
/* "csamtools.pyx":1115
* cdef bam_plbuf_t *buf
@@ -11591,7 +10949,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -11613,9 +10971,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1118
* raise ValueError( "I/O operation on closed file" )
@@ -11624,10 +10982,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*
* if self.isbam:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -11678,23 +11036,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
+ index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed;
+ index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed;
+ index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_6);
- index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed;
+ index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L5_unpacking_done;
- __pyx_L4_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L5_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -11716,7 +11074,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
* if not self._hasIndex(): raise ValueError( "no index available for pileup" )
*
*/
- if (__pyx_v_self->isbam) {
+ if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
/* "csamtools.pyx":1121
*
@@ -11725,7 +11083,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*
* if callback:
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
@@ -11739,9 +11097,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
/* "csamtools.pyx":1123
* if not self._hasIndex(): raise ValueError( "no index available for pileup" )
@@ -11767,9 +11125,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
+ goto __pyx_L12;
}
- __pyx_L9:;
+ __pyx_L12:;
/* "csamtools.pyx":1126
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
@@ -11787,7 +11145,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*
* # finalize pileup
*/
- bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback);
+ bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback);
/* "csamtools.pyx":1132
*
@@ -11806,7 +11164,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
* if has_coord:
*/
bam_plbuf_destroy(__pyx_v_buf);
- goto __pyx_L8;
+ goto __pyx_L11;
}
/*else*/ {
@@ -11828,19 +11186,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
-
- /* "csamtools.pyx":1140
- * start = rstart,
- * end = rend,
- * **kwargs ) # <<<<<<<<<<<<<<
- * else:
- * return IteratorColumnAllRefs(self, **kwargs )
- */
- __pyx_t_5 = PyDict_Copy(((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
+ __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
/* "csamtools.pyx":1137
@@ -11852,9 +11202,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*/
__pyx_t_6 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid)))) {
- __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__tid)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
@@ -11867,9 +11214,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*/
__pyx_t_6 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start)))) {
- __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__start)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
@@ -11882,19 +11226,25 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*/
__pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end)))) {
- __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__end)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnRegion)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "csamtools.pyx":1140
+ * start = rstart,
+ * end = rend,
+ * **kwargs ) # <<<<<<<<<<<<<<
+ * else:
+ * return IteratorColumnAllRefs(self, **kwargs )
+ */
+ if (PyDict_Update(((PyObject *)__pyx_t_5), ((PyObject *)__pyx_v_kwargs)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnRegion)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__pyx_r = __pyx_t_6;
__pyx_t_6 = 0;
goto __pyx_L0;
- goto __pyx_L10;
+ goto __pyx_L13;
}
/*else*/ {
@@ -11907,24 +11257,21 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- __pyx_t_5 = ((PyObject *)__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_INCREF(__pyx_v_self);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
+ __Pyx_GIVEREF(__pyx_v_self);
+ __pyx_t_5 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_r = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_r = __pyx_t_5;
+ __pyx_t_5 = 0;
goto __pyx_L0;
}
- __pyx_L10:;
+ __pyx_L13:;
}
- __pyx_L8:;
- goto __pyx_L6;
+ __pyx_L11:;
+ goto __pyx_L9;
}
/*else*/ {
@@ -11935,13 +11282,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
*
* def close( self ):
*/
- __pyx_t_7 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_Raise(__pyx_t_7, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L6:;
+ __pyx_L9:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -11955,24 +11302,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_26pileup(struct __pyx_obj_9csamtoo
__Pyx_AddTraceback("csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_28close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
-static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("close (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_28close(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1147
* raise NotImplementedError( "pileup of samfiles not implemented yet" )
*
@@ -11981,12 +11317,14 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CY
* closes the :class:`pysam.Samfile`.'''
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_14close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
+static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close", 0);
+ __Pyx_RefNannySetupContext("close");
__Pyx_TraceCall("close", __pyx_f[0], 1147);
/* "csamtools.pyx":1150
@@ -11996,7 +11334,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool
* samclose( self.samfile )
* bam_index_destroy(self.index);
*/
- __pyx_t_1 = (__pyx_v_self->samfile != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":1151
@@ -12006,7 +11344,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool
* bam_index_destroy(self.index);
* self.samfile = NULL
*/
- samclose(__pyx_v_self->samfile);
+ samclose(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile);
/* "csamtools.pyx":1152
* if self.samfile != NULL:
@@ -12015,7 +11353,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool
* self.samfile = NULL
*
*/
- bam_index_destroy(__pyx_v_self->index);
+ bam_index_destroy(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index);
/* "csamtools.pyx":1153
* samclose( self.samfile )
@@ -12024,10 +11362,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool
*
* def __dealloc__( self ):
*/
- __pyx_v_self->samfile = NULL;
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -12036,15 +11374,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_28close(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_7Samfile_30__dealloc__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":1155
* self.samfile = NULL
*
@@ -12053,7 +11382,8 @@ static void __pyx_pw_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self) {
* # note: no doc string
*/
-static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
@@ -12062,7 +11392,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1155);
/* "csamtools.pyx":1159
@@ -12072,7 +11402,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo
* bam_destroy1(self.b)
* if self._filename != NULL: free( self._filename )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -12086,7 +11416,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo
* if self._filename != NULL: free( self._filename )
*
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
/* "csamtools.pyx":1161
* self.close()
@@ -12095,12 +11425,12 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo
*
* cpdef int write( self, AlignedRead read ) except -1:
*/
- __pyx_t_3 = (__pyx_v_self->_filename != NULL);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
if (__pyx_t_3) {
- free(__pyx_v_self->_filename);
- goto __pyx_L3;
+ free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
goto __pyx_L0;
__pyx_L1_error:;
@@ -12120,7 +11450,7 @@ static void __pyx_pf_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_9csamtoo
* write a single :class:`pysam.AlignedRead` to disk.
*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) {
int __pyx_r;
__Pyx_RefNannyDeclarations
@@ -12134,7 +11464,7 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_RefNannySetupContext("write");
__Pyx_TraceCall("write", __pyx_f[0], 1163);
/* Check if called by wrapper */
if (unlikely(__pyx_skip_dispatch)) ;
@@ -12142,9 +11472,9 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_9csamtools_7Samfile_33write)) {
+ if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (void *)&__pyx_pf_9csamtools_7Samfile_16write)) {
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(((PyObject *)__pyx_v_read));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_read));
__Pyx_GIVEREF(((PyObject *)__pyx_v_read));
@@ -12214,23 +11544,6 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_32write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
-static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("write (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_7Samfile_32write(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1163
* if self._filename != NULL: free( self._filename )
*
@@ -12239,7 +11552,9 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, Py
* write a single :class:`pysam.AlignedRead` to disk.
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_16write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
+static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -12247,10 +11562,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtool
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_RefNannySetupContext("write");
__Pyx_TraceCall("write", __pyx_f[0], 1163);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->write(__pyx_v_self, __pyx_v_read, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->write(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read), 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -12269,18 +11585,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_32write(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_34__enter__[] = "Samfile.__enter__(self)";
-static PyObject *__pyx_pw_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__enter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_34__enter__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1174
* return samwrite( self.samfile, read._delegate )
*
@@ -12289,11 +11593,13 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self
*
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_17__enter__[] = "Samfile.__enter__(self)";
+static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__enter__", 0);
+ __Pyx_RefNannySetupContext("__enter__");
__Pyx_TraceCall("__enter__", __pyx_f[0], 1174);
/* "csamtools.pyx":1175
@@ -12304,8 +11610,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csam
* def __exit__(self, exc_type, exc_value, traceback):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -12316,23 +11622,36 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_34__enter__(struct __pyx_obj_9csam
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_36__exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
-static PyObject *__pyx_pw_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- CYTHON_UNUSED PyObject *__pyx_v_exc_type = 0;
- CYTHON_UNUSED PyObject *__pyx_v_exc_value = 0;
- CYTHON_UNUSED PyObject *__pyx_v_traceback = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
- PyObject *__pyx_r = 0;
+/* "csamtools.pyx":1177
+ * return self
+ *
+ * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
+ * self.close()
+ * return False
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_18__exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
+static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_exc_type = 0;
+ PyObject *__pyx_v_exc_value = 0;
+ PyObject *__pyx_v_traceback = 0;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__exit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__exit__");
+ __Pyx_TraceCall("__exit__", __pyx_f[0], 1177);
{
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
@@ -12340,7 +11659,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self,
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_type);
if (likely(values[0])) kw_args--;
@@ -12359,7 +11678,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self,
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -12380,30 +11699,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self,
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_7Samfile_36__exit__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_exc_type, __pyx_v_exc_value, __pyx_v_traceback);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1177
- * return self
- *
- * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
- * self.close()
- * return False
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__exit__", 0);
- __Pyx_TraceCall("__exit__", __pyx_f[0], 1177);
/* "csamtools.pyx":1178
*
@@ -12412,7 +11707,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamt
* return False
*
*/
- __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 = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -12447,17 +11742,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_36__exit__(struct __pyx_obj_9csamt
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_8filename___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1188
* property filename:
* '''number of :term:`filename` associated with this object.'''
@@ -12466,7 +11750,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx
* return self._filename
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -12477,7 +11762,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1188);
/* "csamtools.pyx":1189
@@ -12487,7 +11772,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj
* return self._filename
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -12501,9 +11786,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1190
* def __get__(self):
@@ -12513,7 +11798,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj
* property nreferences:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -12533,17 +11818,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_11nreferences___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1194
* property nreferences:
* '''number of :term:`reference` sequences in the file.'''
@@ -12552,7 +11826,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(PyObject *_
* return self.samfile.header.n_targets
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -12563,7 +11838,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1194);
/* "csamtools.pyx":1195
@@ -12573,7 +11848,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx
* return self.samfile.header.n_targets
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -12587,9 +11862,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1196
* def __get__(self):
@@ -12599,7 +11874,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx
* property references:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -12619,17 +11894,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_10references___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1200
* property references:
* """tuple with the names of :term:`reference` sequences."""
@@ -12638,7 +11902,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_10references_1__get__(PyObject *__
* t = []
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_t = NULL;
long __pyx_v_x;
PyObject *__pyx_r = NULL;
@@ -12653,7 +11918,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1200);
/* "csamtools.pyx":1201
@@ -12663,7 +11928,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -12677,9 +11942,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1202
* def __get__(self):
@@ -12689,7 +11954,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_t = __pyx_t_2;
__pyx_t_2 = 0;
@@ -12700,7 +11965,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
* return tuple(t)
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
/* "csamtools.pyx":1204
@@ -12710,7 +11975,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
* return tuple(t)
*
*/
- __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12724,6 +11992,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
* property lengths:
*/
__Pyx_XDECREF(__pyx_r);
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
@@ -12745,17 +12016,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(struct __pyx_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_7lengths___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1211
* :attr:`pysam.Samfile.references`
* """
@@ -12764,7 +12024,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_
* t = []
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_t = NULL;
long __pyx_v_x;
PyObject *__pyx_r = NULL;
@@ -12779,7 +12040,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1211);
/* "csamtools.pyx":1212
@@ -12789,7 +12050,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -12803,9 +12064,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1213
* def __get__(self):
@@ -12815,7 +12076,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
* t.append( self.samfile.header.target_len[x] )
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_t = __pyx_t_2;
__pyx_t_2 = 0;
@@ -12826,7 +12087,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
* t.append( self.samfile.header.target_len[x] )
* return tuple(t)
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
/* "csamtools.pyx":1215
@@ -12836,7 +12097,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
* return tuple(t)
*
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((__pyx_v_self->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12850,6 +12114,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
* property mapped:
*/
__Pyx_XDECREF(__pyx_r);
+ if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
@@ -12871,17 +12138,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_6mapped___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1221
* """total number of mapped reads in file.
* """
@@ -12890,7 +12146,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self) {
int __pyx_v_tid;
uint32_t __pyx_v_total;
PyObject *__pyx_r = NULL;
@@ -12904,7 +12161,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1221);
/* "csamtools.pyx":1222
@@ -12914,7 +12171,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -12928,9 +12185,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1223
* def __get__(self):
@@ -12939,16 +12196,16 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9
*
* cdef int tid
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
__pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_93), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":1226
*
@@ -12966,7 +12223,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9
* total += pysam_get_mapped( self.index, tid )
* return total
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
/* "csamtools.pyx":1228
@@ -12976,7 +12233,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9
* return total
*
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_mapped(__pyx_v_self->index, __pyx_v_tid));
+ __pyx_v_total = (__pyx_v_total + pysam_get_mapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid));
}
/* "csamtools.pyx":1229
@@ -13007,17 +12264,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_9
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_8unmapped___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1234
* """total number of unmapped reads in file.
* """
@@ -13026,7 +12272,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self) {
int __pyx_v_tid;
uint32_t __pyx_v_total;
PyObject *__pyx_r = NULL;
@@ -13040,7 +12287,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1234);
/* "csamtools.pyx":1235
@@ -13050,7 +12297,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
* cdef int tid
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -13064,9 +12311,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1236
* def __get__(self):
@@ -13075,16 +12322,16 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
* cdef int tid
* cdef uint32_t total = 0
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
__pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_96), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":1238
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
@@ -13102,7 +12349,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
* total += pysam_get_unmapped( self.index, tid )
* # get unmapped reads without coordinates
*/
- __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
+ __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
/* "csamtools.pyx":1240
@@ -13112,7 +12359,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
* # get unmapped reads without coordinates
* total += pysam_get_unmapped( self.index, -1 )
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, __pyx_v_tid));
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid));
}
/* "csamtools.pyx":1242
@@ -13122,7 +12369,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
* return total
*
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, -1));
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, -1));
/* "csamtools.pyx":1243
* # get unmapped reads without coordinates
@@ -13152,17 +12399,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_4text___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1247
* property text:
* '''full contents of the :term:`sam file` header as a string.'''
@@ -13171,7 +12407,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_s
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -13182,7 +12419,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1247);
/* "csamtools.pyx":1248
@@ -13192,7 +12429,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -13206,9 +12443,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1249
* def __get__(self):
@@ -13218,7 +12455,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs
* property header:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_from_string_and_size(__pyx_v_self->samfile->header->text, __pyx_v_self->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_from_string_and_size(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -13238,17 +12475,6 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_6header___get__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1255
* a two-level dictionary.
* '''
@@ -13257,7 +12483,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v
*
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_result = NULL;
PyObject *__pyx_v_t = NULL;
PyObject *__pyx_v_line = NULL;
@@ -13290,7 +12517,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1255);
/* "csamtools.pyx":1256
@@ -13300,7 +12527,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
*
* result = {}
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -13314,9 +12541,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1258
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
@@ -13337,7 +12564,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text
*/
- __pyx_t_4 = (__pyx_v_self->samfile->header->text != NULL);
+ __pyx_t_4 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text != NULL);
if (__pyx_t_4) {
/* "csamtools.pyx":1262
@@ -13347,7 +12574,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* for line in t.split("\n"):
* if not line.strip(): continue
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_t = __pyx_t_2;
__pyx_t_2 = 0;
@@ -13374,10 +12601,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
__pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
__pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
} else {
@@ -13411,10 +12638,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- goto __pyx_L5_continue;
- goto __pyx_L7;
+ goto __pyx_L7_continue;
+ goto __pyx_L9;
}
- __pyx_L7:;
+ __pyx_L9:;
/* "csamtools.pyx":1265
* for line in t.split("\n"):
@@ -13486,7 +12713,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(!__pyx_t_3)) {
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
@@ -13519,15 +12746,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* result[record].append( "\t".join( fields[1:] ) )
* continue
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
__pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L9;
+ goto __pyx_L11;
}
- __pyx_L9:;
+ __pyx_L11:;
/* "csamtools.pyx":1273
* if record == "CO":
@@ -13543,7 +12773,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
@@ -13564,10 +12794,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
*
* # the following is clumsy as generators do not work?
*/
- goto __pyx_L5_continue;
- goto __pyx_L8;
+ goto __pyx_L7_continue;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
/* "csamtools.pyx":1277
*
@@ -13601,10 +12831,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_8)) {
+ if (PyList_CheckExact(__pyx_t_8)) {
if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_8)) break;
__pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
- } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) {
+ } else if (PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
__pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
} else {
@@ -13662,19 +12892,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
- index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L12_unpacking_failed;
+ index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L14_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed;
+ index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L14_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- goto __pyx_L13_unpacking_done;
- __pyx_L12_unpacking_failed:;
+ goto __pyx_L15_unpacking_done;
+ __pyx_L14_unpacking_failed:;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L13_unpacking_done:;
+ __pyx_L15_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_key);
__pyx_v_key = __pyx_t_9;
@@ -13715,7 +12945,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
@@ -13725,7 +12955,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L14;
+ goto __pyx_L16;
}
/* "csamtools.pyx":1284
@@ -13753,7 +12983,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
*/
if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ goto __pyx_L16;
}
/*else*/ {
@@ -13765,7 +12995,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* if VALID_HEADER_TYPES[record] == dict:
*/
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
@@ -13776,7 +13006,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
@@ -13787,7 +13017,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L14:;
+ __pyx_L16:;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
@@ -13817,6 +13047,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* raise ValueError( "multiple '%s' lines are not permitted" % record )
* result[record] = x
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_4 = ((PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
@@ -13830,7 +13063,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_v_record); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
@@ -13840,9 +13073,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ goto __pyx_L18;
}
- __pyx_L16:;
+ __pyx_L18:;
/* "csamtools.pyx":1292
* if record in result:
@@ -13852,7 +13085,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* if record not in result: result[record] = []
*/
if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L15;
+ goto __pyx_L17;
}
/* "csamtools.pyx":1293
@@ -13881,15 +13114,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* result[record].append( x )
*
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
__pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- goto __pyx_L17;
+ goto __pyx_L19;
}
- __pyx_L17:;
+ __pyx_L19:;
/* "csamtools.pyx":1295
* elif VALID_HEADER_TYPES[record] == list:
@@ -13904,10 +13140,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L15;
+ goto __pyx_L17;
}
- __pyx_L15:;
- __pyx_L5_continue:;
+ __pyx_L17:;
+ __pyx_L7_continue:;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -13918,6 +13154,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* sq = []
* for ref, length in zip( self.references, self.lengths ):
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
@@ -13929,7 +13168,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* sq.append( {'LN': length, 'SN': ref } )
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_sq = __pyx_t_2;
__pyx_t_2 = 0;
@@ -13940,12 +13179,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* sq.append( {'LN': length, 'SN': ref } )
* result["SQ"] = sq
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_9);
@@ -13965,10 +13204,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_8)) {
+ if (PyList_CheckExact(__pyx_t_8)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_8)) break;
__pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_8)) {
+ } else if (PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
__pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
} else {
@@ -14010,19 +13249,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_1)->tp_iternext;
- index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L21_unpacking_failed;
+ index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L23_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L21_unpacking_failed;
+ index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L23_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_1), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L22_unpacking_done;
- __pyx_L21_unpacking_failed:;
+ goto __pyx_L24_unpacking_done;
+ __pyx_L23_unpacking_failed:;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L22_unpacking_done:;
+ __pyx_L24_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_2;
@@ -14038,6 +13277,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* result["SQ"] = sq
*
*/
+ if (unlikely(((PyObject *)__pyx_v_sq) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__LN), __pyx_v_length) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -14055,12 +13297,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
* return result
*/
if (PyDict_SetItem(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_sq)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L18;
+ goto __pyx_L20;
}
- __pyx_L18:;
- goto __pyx_L4;
+ __pyx_L20:;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":1309
* result["SQ"] = sq
@@ -14104,29 +13346,50 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(struct __pyx_obj_9
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_38_buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
-static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1311
+ * return result
+ *
+ * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
+ * '''build a header line from *fields* dictionary for *record*'''
+ *
+ */
+
+static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_19_buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
+static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_fields = 0;
PyObject *__pyx_v_record = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_line = NULL;
+ PyObject *__pyx_v_key = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_buildLine (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ Py_ssize_t __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_buildLine");
+ __Pyx_TraceCall("_buildLine", __pyx_f[0], 1311);
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields);
if (likely(values[0])) kw_args--;
@@ -14139,7 +13402,7 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_sel
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -14158,38 +13421,6 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_sel
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_7Samfile_38_buildLine(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_fields, __pyx_v_record);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1311
- * return result
- *
- * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
- * '''build a header line from *fields* dictionary for *record*'''
- *
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record) {
- PyObject *__pyx_v_line = NULL;
- PyObject *__pyx_v_key = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- PyObject *(*__pyx_t_6)(PyObject *);
- PyObject *__pyx_t_7 = NULL;
- int __pyx_t_8;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildLine", 0);
- __Pyx_TraceCall("_buildLine", __pyx_f[0], 1311);
/* "csamtools.pyx":1315
*
@@ -14201,7 +13432,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_109), __pyx_v_record); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -14225,8 +13456,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
* # user tags
* elif record.islower():
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_4 = PyList_Append(__pyx_v_line, __pyx_v_fields); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
/* "csamtools.pyx":1320
@@ -14253,7 +13487,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
* # defined tags
*/
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
@@ -14270,10 +13504,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
__pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
__pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
} else {
@@ -14298,10 +13532,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
* # defined tags
* else:
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
@@ -14309,7 +13546,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
@@ -14323,7 +13560,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L3;
+ goto __pyx_L6;
}
/*else*/ {
@@ -14349,10 +13586,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
__pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
__pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
} else {
@@ -14387,10 +13624,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
* # write user fields
* for key in fields:
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
@@ -14398,7 +13638,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
@@ -14410,9 +13650,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- goto __pyx_L8;
+ goto __pyx_L11;
}
- __pyx_L8:;
+ __pyx_L11:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -14432,10 +13672,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
__pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
__pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
} else {
@@ -14477,10 +13717,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
*
* return "\t".join( line )
*/
+ if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_7 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
@@ -14488,7 +13731,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
@@ -14500,13 +13743,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L11;
+ goto __pyx_L14;
}
- __pyx_L11:;
+ __pyx_L14:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1334
* line.append( "%s:%s" % (key, str(fields[key])))
@@ -14519,7 +13762,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(((PyObject *)__pyx_v_line));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_line));
__Pyx_GIVEREF(((PyObject *)__pyx_v_line));
@@ -14596,7 +13839,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildHeader", 0);
+ __Pyx_RefNannySetupContext("_buildHeader");
__Pyx_TraceCall("_buildHeader", __pyx_f[0], 1336);
/* "csamtools.pyx":1342
@@ -14607,7 +13850,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* # check if hash exists
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_lines = __pyx_t_1;
__pyx_t_1 = 0;
@@ -14639,10 +13882,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
__pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
- } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
__pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
} else {
@@ -14725,7 +13968,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
@@ -14740,7 +13983,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -14771,10 +14014,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* else:
* for fields in new_header[record]:
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_data);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_data);
__Pyx_GIVEREF(__pyx_v_data);
@@ -14810,10 +14056,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_6)) {
+ if (PyList_CheckExact(__pyx_t_6)) {
if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_6)) break;
__pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_6)) {
+ } else if (PyTuple_CheckExact(__pyx_t_6)) {
if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
__pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
} else {
@@ -14838,10 +14084,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
*
* # then: user tags (lower case), sorted alphabetically
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
@@ -14877,7 +14126,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
@@ -14894,10 +14143,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
for (;;) {
- if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
__pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
- } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
__pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
} else {
@@ -14994,10 +14243,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* else:
* for fields in new_header[record]:
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_data);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_data);
__Pyx_GIVEREF(__pyx_v_data);
@@ -15033,10 +14285,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_1)) break;
__pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) {
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
__pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
} else {
@@ -15061,10 +14313,13 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
*
* text = "\n".join(lines) + "\n"
*/
+ if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
@@ -15095,7 +14350,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_v_lines));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_lines));
__Pyx_GIVEREF(((PyObject *)__pyx_v_lines));
@@ -15187,7 +14442,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* try:
*/
__pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__pyx_v_seqs = __pyx_t_7;
__pyx_t_7 = 0;
@@ -15210,10 +14465,10 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
- if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
__pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
- } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
__pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
} else {
@@ -15252,12 +14507,15 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* except KeyError:
* raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*/
+ if (unlikely(((PyObject *)__pyx_v_seqs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ }
__pyx_t_7 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_2 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
@@ -15300,7 +14558,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* dest.n_targets = len(seqs)
*/
__pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
- __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_11));
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
@@ -15311,7 +14569,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_GOTREF(((PyObject *)__pyx_t_11));
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
__pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
- __Pyx_GOTREF(__pyx_t_18);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_18));
PyTuple_SET_ITEM(__pyx_t_18, 0, ((PyObject *)__pyx_t_11));
__Pyx_GIVEREF(((PyObject *)__pyx_t_11));
__pyx_t_11 = 0;
@@ -15349,6 +14607,9 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
* dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*/
+ if (unlikely(((PyObject *)__pyx_v_seqs) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs));
__pyx_v_dest->n_targets = __pyx_t_3;
@@ -15528,17 +14789,6 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_40__iter__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1411
* ## Possible solutions: deprecate or open new file handle
* ###############################################################
@@ -15547,7 +14797,8 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self)
* if not self.isbam and self.samfile.header.n_targets == 0:
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -15559,7 +14810,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1411);
/* "csamtools.pyx":1412
@@ -15569,7 +14820,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header")
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -15583,9 +14834,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1413
* def __iter__(self):
@@ -15594,9 +14845,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt
* raise NotImplementedError( "can not iterate over samfile without header")
* return self
*/
- __pyx_t_4 = (!__pyx_v_self->isbam);
+ __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
if (__pyx_t_4) {
- __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
__pyx_t_5 = __pyx_t_3;
} else {
__pyx_t_5 = __pyx_t_4;
@@ -15615,9 +14866,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":1415
* if not self.isbam and self.samfile.header.n_targets == 0:
@@ -15627,8 +14878,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_40__iter__(struct __pyx_obj_9csamt
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -15657,7 +14908,7 @@ static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtool
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1417);
/* "csamtools.pyx":1418
@@ -15689,7 +14940,7 @@ static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1420);
/* "csamtools.pyx":1425
@@ -15709,19 +14960,6 @@ static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_42__next__[] = "\n python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile_42__next__;
-static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7Samfile_42__next__(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1427
* return samread(self.samfile, self.b)
*
@@ -15730,7 +14968,10 @@ static PyObject *__pyx_pw_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self)
* python version of next().
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_7Samfile_21__next__[] = "\n python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile_21__next__;
+static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -15740,7 +14981,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1427);
/* "csamtools.pyx":1432
@@ -15750,7 +14991,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = samread(__pyx_v_self->samfile, __pyx_v_self->b);
+ __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
/* "csamtools.pyx":1433
* cdef int ret
@@ -15770,12 +15011,12 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
@@ -15789,7 +15030,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -15804,24 +15045,42 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_42__next__(struct __pyx_obj_9csamt
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1481
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
+
+static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_tid;
int __pyx_v_beg;
int __pyx_v_end;
int __pyx_v_reopen;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481);
{
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -15831,7 +15090,7 @@ static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
@@ -15861,19 +15120,7 @@ static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- if (values[4]) {
- } else {
-
- /* "csamtools.pyx":1481
- * """
- *
- * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
- __pyx_v_reopen = ((int)1);
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -15905,31 +15152,6 @@ static int __pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_beg, __pyx_v_end, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481);
/* "csamtools.pyx":1483
* def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ):
@@ -15960,9 +15182,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1486
* raise ValueError( "I/O operation on closed file" )
@@ -15993,9 +15215,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
+ __pyx_L7:;
/* "csamtools.pyx":1491
* # makes sure that samfile stays alive as long as the
@@ -16006,9 +15228,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile = __pyx_v_samfile;
/* "csamtools.pyx":1493
* self.samfile = samfile
@@ -16020,7 +15242,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L5;
+ goto __pyx_L8;
}
/*else*/ {
@@ -16034,7 +15256,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L5:;
+ __pyx_L8:;
/* "csamtools.pyx":1498
* # reopen the file - note that this makes the iterator
@@ -16068,7 +15290,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
* assert self.fp != NULL
*/
__pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
/* "csamtools.pyx":1501
* store = StderrStore()
@@ -16092,7 +15314,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
@@ -16105,8 +15327,8 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
* else:
* self.fp = self.samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L6;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L9;
}
/*else*/ {
@@ -16117,7 +15339,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
* self.owns_samfile = False
*
*/
- __pyx_v_self->fp = __pyx_v_self->samfile->samfile;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->samfile;
/* "csamtools.pyx":1506
* else:
@@ -16126,9 +15348,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
*
* self.retval = 0
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L6:;
+ __pyx_L9:;
/* "csamtools.pyx":1508
* self.owns_samfile = False
@@ -16137,7 +15359,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
*
* self.iter = bam_iter_query(self.samfile.index,
*/
- __pyx_v_self->retval = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval = 0;
/* "csamtools.pyx":1510
* self.retval = 0
@@ -16146,7 +15368,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
* tid,
* beg,
*/
- __pyx_v_self->iter = bam_iter_query(__pyx_v_self->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter = bam_iter_query(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
/* "csamtools.pyx":1514
* beg,
@@ -16155,7 +15377,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
*
* def __iter__(self):
*/
- __pyx_v_self->b = bam_init1();
+ ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b = bam_init1();
__pyx_r = 0;
goto __pyx_L0;
@@ -16172,17 +15394,6 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1516
* self.b = bam_init1()
*
@@ -16191,11 +15402,12 @@ static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__p
*
*/
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1516);
/* "csamtools.pyx":1517
@@ -16206,8 +15418,8 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -16230,7 +15442,7 @@ static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_ob
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1519);
/* "csamtools.pyx":1520
@@ -16262,7 +15474,7 @@ static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamto
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1522);
/* "csamtools.pyx":1524
@@ -16280,19 +15492,6 @@ static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamto
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_17IteratorRowRegion_4__next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__;
-static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_17IteratorRowRegion_4__next__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1528
* self.b)
*
@@ -16301,7 +15500,10 @@ static PyObject *__pyx_pw_9csamtools_17IteratorRowRegion_5__next__(PyObject *__p
* """
*/
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_17IteratorRowRegion_2__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__;
+static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -16310,7 +15512,7 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1528);
/* "csamtools.pyx":1531
@@ -16320,7 +15522,7 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_
* if self.retval < 0: raise StopIteration
* return makeAlignedRead( self.b )
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
+ ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
/* "csamtools.pyx":1532
* """
@@ -16329,13 +15531,13 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_
* return makeAlignedRead( self.b )
*
*/
- __pyx_t_1 = (__pyx_v_self->retval < 0);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval < 0);
if (__pyx_t_1) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1533
* self.cnext()
@@ -16345,7 +15547,7 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_
* def __dealloc__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -16364,15 +15566,6 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":1535
* return makeAlignedRead( self.b )
*
@@ -16381,10 +15574,11 @@ static void __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx
* bam_iter_destroy( self.iter )
*/
-static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static void __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1535);
/* "csamtools.pyx":1536
@@ -16394,7 +15588,7 @@ static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_ob
* bam_iter_destroy( self.iter )
* if self.owns_samfile: samclose( self.fp )
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b);
/* "csamtools.pyx":1537
* def __dealloc__(self):
@@ -16403,7 +15597,7 @@ static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_ob
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_iter_destroy(__pyx_v_self->iter);
+ bam_iter_destroy(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter);
/* "csamtools.pyx":1538
* bam_destroy1(self.b)
@@ -16412,38 +15606,56 @@ static void __pyx_pf_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_ob
*
* cdef class IteratorRowAll(IteratorRow):
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1550
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
+
+static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_reopen;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1550);
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
@@ -16455,19 +15667,7 @@ static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_sel
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- if (values[1]) {
- } else {
-
- /* "csamtools.pyx":1550
- * """
- *
- * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
- __pyx_v_reopen = ((int)1);
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -16493,31 +15693,6 @@ static int __pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_sel
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_14IteratorRowAll___cinit__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1550);
/* "csamtools.pyx":1552
* def __cinit__(self, Samfile samfile, int reopen = True ):
@@ -16548,9 +15723,9 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1555
* raise ValueError( "I/O operation on closed file" )
@@ -16562,7 +15737,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L4;
+ goto __pyx_L7;
}
/*else*/ {
@@ -16576,7 +15751,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L4:;
+ __pyx_L7:;
/* "csamtools.pyx":1559
*
@@ -16610,7 +15785,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
* assert self.fp != NULL
*/
__pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
/* "csamtools.pyx":1562
* store = StderrStore()
@@ -16634,7 +15809,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
@@ -16647,8 +15822,8 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
* else:
* self.fp = samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L5;
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L8;
}
/*else*/ {
@@ -16659,7 +15834,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
* self.owns_samfile = False
*
*/
- __pyx_v_self->fp = __pyx_v_samfile->samfile;
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
/* "csamtools.pyx":1567
* else:
@@ -16668,9 +15843,9 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
*
* # allocate memory for alignment
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L5:;
+ __pyx_L8:;
/* "csamtools.pyx":1570
*
@@ -16679,7 +15854,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
*
* def __iter__(self):
*/
- __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
__pyx_r = 0;
goto __pyx_L0;
@@ -16696,17 +15871,6 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_9csam
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_14IteratorRowAll_2__iter__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1572
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
@@ -16715,11 +15879,12 @@ static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_
*
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1572);
/* "csamtools.pyx":1573
@@ -16730,8 +15895,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -16754,7 +15919,7 @@ static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1575);
/* "csamtools.pyx":1576
@@ -16786,7 +15951,7 @@ static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1578);
/* "csamtools.pyx":1580
@@ -16806,19 +15971,6 @@ static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorRowAll_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__;
-static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_14IteratorRowAll_4__next__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1582
* return samread(self.fp, self.b)
*
@@ -16827,7 +15979,10 @@ static PyObject *__pyx_pw_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_
*
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorRowAll_2__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__;
+static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -16837,7 +15992,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1582);
/* "csamtools.pyx":1588
@@ -16847,7 +16002,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_self->b);
+ __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp, ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
/* "csamtools.pyx":1589
* cdef int ret
@@ -16867,12 +16022,12 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
@@ -16886,7 +16041,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -16901,15 +16056,6 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":1594
* raise StopIteration
*
@@ -16918,10 +16064,11 @@ static void __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_
* if self.owns_samfile: samclose( self.fp )
*/
-static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+static void __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1594);
/* "csamtools.pyx":1595
@@ -16931,7 +16078,7 @@ static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
/* "csamtools.pyx":1596
* def __dealloc__(self):
@@ -16940,43 +16087,58 @@ static void __pyx_pf_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_9
*
* cdef class IteratorRowAllRefs(IteratorRow):
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1602
+ * """
+ *
+ * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
+ * assert samfile._isOpen()
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
+ */
+
+static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1602);
{
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
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 = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -16994,36 +16156,6 @@ static int __pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self), __pyx_v_samfile);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1602
- * """
- *
- * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
- * assert samfile._isOpen()
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
- */
-
-static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1602);
/* "csamtools.pyx":1603
*
@@ -17067,9 +16199,9 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1605
* assert samfile._isOpen()
@@ -17080,9 +16212,9 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile = __pyx_v_samfile;
/* "csamtools.pyx":1606
* if not samfile._hasIndex(): raise ValueError("no index available for fetch")
@@ -17091,7 +16223,7 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9
*
* def nextiter(self):
*/
- __pyx_v_self->tid = -1;
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = -1;
__pyx_r = 0;
goto __pyx_L0;
@@ -17106,18 +16238,6 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_9
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_18IteratorRowAllRefs_2nextiter[] = "IteratorRowAllRefs.nextiter(self)";
-static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("nextiter (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1608
* self.tid = -1
*
@@ -17126,7 +16246,9 @@ static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__
*
*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter[] = "IteratorRowAllRefs.nextiter(self)";
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -17135,7 +16257,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("nextiter", 0);
+ __Pyx_RefNannySetupContext("nextiter");
__Pyx_TraceCall("nextiter", __pyx_f[0], 1608);
/* "csamtools.pyx":1609
@@ -17145,13 +16267,13 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx
*
* def __iter__(self):
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self->samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
+ __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_int_0);
@@ -17165,9 +16287,9 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GOTREF(__pyx_v_self->rowiter);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->rowiter));
- __pyx_v_self->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_1);
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter));
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_1);
__pyx_t_1 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -17184,17 +16306,6 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1611
* self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29)
*
@@ -17203,11 +16314,12 @@ static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__
*
*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1611);
/* "csamtools.pyx":1612
@@ -17218,8 +16330,8 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx
* def __next__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -17230,19 +16342,6 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__;
-static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1614
* return self
*
@@ -17251,7 +16350,10 @@ static PyObject *__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__
*
*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
+static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -17263,7 +16365,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1614);
/* "csamtools.pyx":1620
@@ -17273,7 +16375,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
* if not self.samfile.nreferences:
* raise StopIteration
*/
- __pyx_t_1 = (__pyx_v_self->tid == -1);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid == -1);
if (__pyx_t_1) {
/* "csamtools.pyx":1621
@@ -17283,7 +16385,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
* raise StopIteration
* self.tid = 0
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -17299,9 +16401,9 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":1623
* if not self.samfile.nreferences:
@@ -17310,7 +16412,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
* self.nextiter()
*
*/
- __pyx_v_self->tid = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = 0;
/* "csamtools.pyx":1624
* raise StopIteration
@@ -17319,15 +16421,15 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
*
* while 1:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1626
* self.nextiter()
@@ -17346,7 +16448,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
*
* # If current iterator is not exhausted, return aligned read
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)__pyx_v_self->rowiter->__pyx_vtab)->cnext(__pyx_v_self->rowiter);
+ ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
/* "csamtools.pyx":1630
*
@@ -17355,7 +16457,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
* return makeAlignedRead(self.rowiter.b)
*
*/
- __pyx_t_3 = (__pyx_v_self->rowiter->retval > 0);
+ __pyx_t_3 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->retval > 0);
if (__pyx_t_3) {
/* "csamtools.pyx":1631
@@ -17366,14 +16468,14 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
* self.tid += 1
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L7;
+ goto __pyx_L9;
}
- __pyx_L7:;
+ __pyx_L9:;
/* "csamtools.pyx":1633
* return makeAlignedRead(self.rowiter.b)
@@ -17382,7 +16484,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
*
* # Otherwise, proceed to next reference or stop
*/
- __pyx_v_self->tid = (__pyx_v_self->tid + 1);
+ ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid + 1);
/* "csamtools.pyx":1636
*
@@ -17391,9 +16493,9 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
* self.nextiter()
* else:
*/
- __pyx_t_4 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
@@ -17410,13 +16512,13 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
* else:
* raise StopIteration
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L8;
+ goto __pyx_L10;
}
/*else*/ {
@@ -17430,7 +16532,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L8:;
+ __pyx_L10:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -17448,22 +16550,40 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1647
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
+
+static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
PyObject *__pyx_v_positions = 0;
int __pyx_v_reopen;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1647);
{
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
@@ -17471,7 +16591,7 @@ static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
@@ -17489,19 +16609,7 @@ static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- if (values[2]) {
- } else {
-
- /* "csamtools.pyx":1647
- * """
- *
- * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
- __pyx_v_reopen = ((int)1);
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -17529,31 +16637,6 @@ static int __pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self), __pyx_v_samfile, __pyx_v_positions, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1647);
/* "csamtools.pyx":1649
* def __cinit__(self, Samfile samfile, positions, int reopen = True ):
@@ -17584,9 +16667,9 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1652
* raise ValueError( "I/O operation on closed file" )
@@ -17617,9 +16700,9 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(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 = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
+ __pyx_L7:;
/* "csamtools.pyx":1655
* raise ValueError( "I/O operation on closed file" )
@@ -17677,7 +16760,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
* assert self.fp != NULL
*/
__pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
/* "csamtools.pyx":1662
* store = StderrStore()
@@ -17701,7 +16784,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
@@ -17714,8 +16797,8 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
* else:
* self.fp = samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L5;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L8;
}
/*else*/ {
@@ -17726,7 +16809,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
* self.owns_samfile = False
*
*/
- __pyx_v_self->fp = __pyx_v_samfile->samfile;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
/* "csamtools.pyx":1667
* else:
@@ -17735,9 +16818,9 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
*
* # allocate memory for alignment
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L5:;
+ __pyx_L8:;
/* "csamtools.pyx":1670
*
@@ -17746,7 +16829,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
*
* self.positions = positions
*/
- __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
/* "csamtools.pyx":1672
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
@@ -17757,9 +16840,9 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
*/
__Pyx_INCREF(__pyx_v_positions);
__Pyx_GIVEREF(__pyx_v_positions);
- __Pyx_GOTREF(__pyx_v_self->positions);
- __Pyx_DECREF(__pyx_v_self->positions);
- __pyx_v_self->positions = __pyx_v_positions;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
+ __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions = __pyx_v_positions;
/* "csamtools.pyx":1673
*
@@ -17768,7 +16851,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
*
* def __iter__(self):
*/
- __pyx_v_self->current_pos = 0;
+ ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->current_pos = 0;
__pyx_r = 0;
goto __pyx_L0;
@@ -17785,17 +16868,6 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1675
* self.current_pos = 0
*
@@ -17804,11 +16876,12 @@ static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_3__iter__(PyObject *
*
*/
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1675);
/* "csamtools.pyx":1676
@@ -17819,8 +16892,8 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__iter__(struct __p
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -17843,7 +16916,7 @@ static bam1_t *__pyx_f_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_RefNannySetupContext("getCurrent");
__Pyx_TraceCall("getCurrent", __pyx_f[0], 1678);
/* "csamtools.pyx":1679
@@ -17882,7 +16955,7 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1681);
/* "csamtools.pyx":1685
@@ -17948,19 +17021,6 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_20IteratorRowSelection_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__;
-static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_20IteratorRowSelection_4__next__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1691
* return samread(self.fp, self.b)
*
@@ -17969,7 +17029,10 @@ static PyObject *__pyx_pw_9csamtools_20IteratorRowSelection_5__next__(PyObject *
*
*/
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_20IteratorRowSelection_2__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__;
+static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -17979,7 +17042,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1691);
/* "csamtools.pyx":1697
@@ -17989,7 +17052,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __p
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = ((struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
+ __pyx_v_ret = ((struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *)((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
/* "csamtools.pyx":1698
*
@@ -18009,12 +17072,12 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __p
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
@@ -18028,7 +17091,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __p
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -18043,15 +17106,6 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_4__next__(struct __p
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":1703
* raise StopIteration
*
@@ -18060,10 +17114,11 @@ static void __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__
* if self.owns_samfile: samclose( self.fp )
*/
-static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1703);
/* "csamtools.pyx":1704
@@ -18073,7 +17128,7 @@ static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_destroy1(__pyx_v_self->b);
+ bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b);
/* "csamtools.pyx":1705
* def __dealloc__(self):
@@ -18082,11 +17137,11 @@ static void __pyx_pf_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx
*
* ##-------------------------------------------------------------------
*/
- 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();
@@ -18105,7 +17160,7 @@ static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_all", 0);
+ __Pyx_RefNannySetupContext("__advance_all");
__Pyx_TraceCall("__advance_all", __pyx_f[0], 1710);
/* "csamtools.pyx":1714
@@ -18163,7 +17218,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
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);
/* "csamtools.pyx":1722
@@ -18298,7 +17353,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
__pyx_t_5 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
@@ -18309,7 +17364,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
__Pyx_GIVEREF(((PyObject *)__pyx_t_5));
__pyx_t_5 = 0;
@@ -18507,36 +17562,50 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1813
+ * '''
+ *
+ * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK )
+ */
+
+static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
PyObject *__pyx_v_kwargs = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1813);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -18555,36 +17624,6 @@ static int __pyx_pw_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_sel
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_14IteratorColumn___cinit__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1813
- * '''
- *
- * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- * self.mask = kwargs.get("mask", BAM_DEF_MASK )
- */
-
-static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1813);
/* "csamtools.pyx":1814
*
@@ -18595,9 +17634,9 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile = __pyx_v_samfile;
/* "csamtools.pyx":1815
* def __cinit__( self, Samfile samfile, **kwargs ):
@@ -18606,6 +17645,9 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.fastafile = kwargs.get( "fastafile", None )
* self.stepper = kwargs.get( "stepper", None )
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = PyInt_FromLong(BAM_DEF_MASK); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__mask), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -18613,7 +17655,7 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_self->mask = __pyx_t_3;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->mask = __pyx_t_3;
/* "csamtools.pyx":1816
* self.samfile = samfile
@@ -18622,13 +17664,16 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.stepper = kwargs.get( "stepper", None )
* self.max_depth = kwargs.get( "max_depth", 8000 )
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__fastafile), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_Fastafile))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_v_self->fastafile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
- __pyx_v_self->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_t_2);
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_t_2);
__pyx_t_2 = 0;
/* "csamtools.pyx":1817
@@ -18638,12 +17683,15 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.max_depth = kwargs.get( "max_depth", 8000 )
* self.iterdata.seq = NULL
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__stepper), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_v_self->stepper);
- __Pyx_DECREF(__pyx_v_self->stepper);
- __pyx_v_self->stepper = __pyx_t_2;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
+ __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper = __pyx_t_2;
__pyx_t_2 = 0;
/* "csamtools.pyx":1818
@@ -18653,11 +17701,14 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.iterdata.seq = NULL
* self.tid = 0
*/
+ if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__max_depth), __pyx_int_8000); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_self->max_depth = __pyx_t_3;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->max_depth = __pyx_t_3;
/* "csamtools.pyx":1819
* self.stepper = kwargs.get( "stepper", None )
@@ -18666,7 +17717,7 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.tid = 0
* self.pos = 0
*/
- __pyx_v_self->iterdata.seq = NULL;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
/* "csamtools.pyx":1820
* self.max_depth = kwargs.get( "max_depth", 8000 )
@@ -18675,7 +17726,7 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.pos = 0
* self.n_plp = 0
*/
- __pyx_v_self->tid = 0;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->tid = 0;
/* "csamtools.pyx":1821
* self.iterdata.seq = NULL
@@ -18684,7 +17735,7 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.n_plp = 0
* self.plp = NULL
*/
- __pyx_v_self->pos = 0;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pos = 0;
/* "csamtools.pyx":1822
* self.tid = 0
@@ -18693,7 +17744,7 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.plp = NULL
* self.pileup_iter = <bam_plp_t>NULL
*/
- __pyx_v_self->n_plp = 0;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->n_plp = 0;
/* "csamtools.pyx":1823
* self.pos = 0
@@ -18702,7 +17753,7 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
* self.pileup_iter = <bam_plp_t>NULL
*
*/
- __pyx_v_self->plp = NULL;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->plp = NULL;
/* "csamtools.pyx":1824
* self.n_plp = 0
@@ -18711,7 +17762,7 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
*
*
*/
- __pyx_v_self->pileup_iter = NULL;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
__pyx_r = 0;
goto __pyx_L0;
@@ -18721,22 +17772,12 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_9csam
__Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_2__iter__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1827
*
*
@@ -18745,11 +17786,12 @@ static PyObject *__pyx_pw_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_
*
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_RefNannySetupContext("__iter__");
__Pyx_TraceCall("__iter__", __pyx_f[0], 1827);
/* "csamtools.pyx":1828
@@ -18760,8 +17802,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj
* cdef int cnext(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self));
- __pyx_r = ((PyObject *)__pyx_v_self);
+ __Pyx_INCREF(__pyx_v_self);
+ __pyx_r = __pyx_v_self;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -18784,7 +17826,7 @@ static int __pyx_f_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_9csamtools
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_RefNannySetupContext("cnext");
__Pyx_TraceCall("cnext", __pyx_f[0], 1830);
/* "csamtools.pyx":1836
@@ -18814,7 +17856,7 @@ static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9c
char *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getSequence", 0);
+ __Pyx_RefNannySetupContext("getSequence");
__Pyx_TraceCall("getSequence", __pyx_f[0], 1841);
/* "csamtools.pyx":1844
@@ -18834,17 +17876,6 @@ static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1848
* property seq_len:
* '''current sequence length.'''
@@ -18853,7 +17884,8 @@ static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject
* def addReference( self, Fastafile fastafile ):
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -18861,10 +17893,10 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 1848);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -18883,23 +17915,6 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(struct __
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorColumn_4addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("addReference (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_4addReference(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_fastafile));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1850
* def __get__(self): return self.iterdata.seq_len
*
@@ -18908,13 +17923,19 @@ static PyObject *__pyx_pw_9csamtools_14IteratorColumn_5addReference(PyObject *__
* add reference sequences in *fastafile* to iterator.'''
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_9csamtools_Fastafile *__pyx_v_fastafile) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorColumn_2addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("addReference", 0);
+ __Pyx_RefNannySetupContext("addReference");
__Pyx_TraceCall("addReference", __pyx_f[0], 1850);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":1853
* '''
@@ -18923,11 +17944,11 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
* self.iterdata.tid = -1
*/
- __Pyx_INCREF(((PyObject *)__pyx_v_fastafile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_fastafile));
- __Pyx_GOTREF(__pyx_v_self->fastafile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
- __pyx_v_self->fastafile = __pyx_v_fastafile;
+ __Pyx_INCREF(__pyx_v_fastafile);
+ __Pyx_GIVEREF(__pyx_v_fastafile);
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_fastafile);
/* "csamtools.pyx":1854
* add reference sequences in *fastafile* to iterator.'''
@@ -18936,12 +17957,12 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx
* self.iterdata.tid = -1
* self.iterdata.fastafile = self.fastafile.fastafile
*/
- __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
if (__pyx_t_1) {
- free(__pyx_v_self->iterdata.seq);
- goto __pyx_L3;
+ free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1855
* self.fastafile = fastafile
@@ -18950,7 +17971,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx
* self.iterdata.fastafile = self.fastafile.fastafile
*
*/
- __pyx_v_self->iterdata.tid = -1;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.tid = -1;
/* "csamtools.pyx":1856
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
@@ -18959,27 +17980,20 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_4addReference(struct __pyx
*
* def hasReference( self ):
*/
- __pyx_v_self->iterdata.fastafile = __pyx_v_self->fastafile->fastafile;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.fastafile = ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile->fastafile;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("csamtools.IteratorColumn.addReference", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorColumn_6hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
-static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("hasReference (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_14IteratorColumn_6hasReference(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1858
* self.iterdata.fastafile = self.fastafile.fastafile
*
@@ -18988,11 +18002,13 @@ static PyObject *__pyx_pw_9csamtools_14IteratorColumn_7hasReference(PyObject *__
* return true if iterator is associated with a reference'''
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_14IteratorColumn_3hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
+static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("hasReference", 0);
+ __Pyx_RefNannySetupContext("hasReference");
__Pyx_TraceCall("hasReference", __pyx_f[0], 1858);
/* "csamtools.pyx":1861
@@ -19003,8 +18019,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_6hasReference(struct __pyx
* cdef setMask( self, mask ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->fastafile));
- __pyx_r = ((PyObject *)__pyx_v_self->fastafile);
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
+ __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -19031,7 +18047,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setMask", 0);
+ __Pyx_RefNannySetupContext("setMask");
__Pyx_TraceCall("setMask", __pyx_f[0], 1863);
/* "csamtools.pyx":1868
@@ -19089,7 +18105,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setupIteratorData", 0);
+ __Pyx_RefNannySetupContext("setupIteratorData");
__Pyx_TraceCall("setupIteratorData", __pyx_f[0], 1871);
if (__pyx_optional_args) {
if (__pyx_optional_args->__pyx_n > 0) {
@@ -19113,7 +18129,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
__pyx_t_4 = PyInt_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
__Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_self->samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
@@ -19272,7 +18288,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
__pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_127), __pyx_v_self->stepper); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
@@ -19351,7 +18367,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_RefNannySetupContext("reset");
__Pyx_TraceCall("reset", __pyx_f[0], 1901);
/* "csamtools.pyx":1907
@@ -19362,7 +18378,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
*
*/
__pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self->samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
@@ -19378,7 +18394,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
__pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -19472,15 +18488,6 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":1919
* bam_plp_reset(self.pileup_iter)
*
@@ -19489,11 +18496,12 @@ static void __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_
* # not been fully consumed
*/
-static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+static void __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 1919);
/* "csamtools.pyx":1922
@@ -19503,7 +18511,7 @@ static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter)
*/
- __pyx_t_1 = (__pyx_v_self->pileup_iter != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter != ((bam_plp_t)NULL));
if (__pyx_t_1) {
/* "csamtools.pyx":1923
@@ -19513,7 +18521,7 @@ static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9
* bam_plp_destroy(self.pileup_iter)
* self.pileup_iter = <bam_plp_t>NULL
*/
- bam_plp_reset(__pyx_v_self->pileup_iter);
+ bam_plp_reset(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
/* "csamtools.pyx":1924
* if self.pileup_iter != <bam_plp_t>NULL:
@@ -19522,7 +18530,7 @@ static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9
* self.pileup_iter = <bam_plp_t>NULL
*
*/
- bam_plp_destroy(__pyx_v_self->pileup_iter);
+ bam_plp_destroy(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
/* "csamtools.pyx":1925
* bam_plp_reset(self.pileup_iter)
@@ -19531,10 +18539,10 @@ static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9
*
* if self.iterdata.seq != NULL:
*/
- __pyx_v_self->pileup_iter = NULL;
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":1927
* self.pileup_iter = <bam_plp_t>NULL
@@ -19543,7 +18551,7 @@ static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9
* free(self.iterdata.seq)
* self.iterdata.seq = NULL
*/
- __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":1928
@@ -19553,7 +18561,7 @@ static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9
* self.iterdata.seq = NULL
*
*/
- free(__pyx_v_self->iterdata.seq);
+ free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
/* "csamtools.pyx":1929
* if self.iterdata.seq != NULL:
@@ -19562,36 +18570,49 @@ static void __pyx_pf_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_9
*
* cdef class IteratorColumnRegion(IteratorColumn):
*/
- __pyx_v_self->iterdata.seq = NULL;
- goto __pyx_L4;
+ ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* "csamtools.pyx":1934
+ * '''iterates over a region only.
+ * '''
+ * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
+ * int tid = 0,
+ * int start = 0,
+ */
+
+static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_tid;
int __pyx_v_start;
int __pyx_v_end;
int __pyx_v_truncate;
- CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__truncate,0};
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__truncate,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1934);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -19601,7 +18622,7 @@ static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
@@ -19628,31 +18649,7 @@ static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- if (values[1]) {
- } else {
- __pyx_v_tid = ((int)0);
- }
- if (values[2]) {
- } else {
- __pyx_v_start = ((int)0);
- }
- if (values[3]) {
- } else {
- __pyx_v_end = __pyx_k_128;
- }
- if (values[4]) {
- } else {
-
- /* "csamtools.pyx":1938
- * int start = 0,
- * int end = max_pos,
- * int truncate = False, # <<<<<<<<<<<<<<
- * **kwargs ):
- *
- */
- __pyx_v_truncate = ((int)0);
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -19684,6 +18681,14 @@ static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx
if (values[4]) {
__pyx_v_truncate = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_truncate == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
+
+ /* "csamtools.pyx":1938
+ * int start = 0,
+ * int end = max_pos,
+ * int truncate = False, # <<<<<<<<<<<<<<
+ * **kwargs ):
+ *
+ */
__pyx_v_truncate = ((int)0);
}
}
@@ -19697,35 +18702,6 @@ static int __pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end, __pyx_v_truncate, __pyx_v_kwargs);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1934
- * '''iterates over a region only.
- * '''
- * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
- * int tid = 0,
- * int start = 0,
- */
-
-static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1934);
/* "csamtools.pyx":1942
*
@@ -19736,7 +18712,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj
*/
__pyx_t_2.__pyx_n = 1;
__pyx_t_2.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -19747,7 +18723,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj
* self.end = end
* self.truncate = truncate
*/
- __pyx_v_self->start = __pyx_v_start;
+ ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start = __pyx_v_start;
/* "csamtools.pyx":1944
* self.setupIteratorData( tid, start, end, 1 )
@@ -19756,7 +18732,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj
* self.truncate = truncate
*
*/
- __pyx_v_self->end = __pyx_v_end;
+ ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->end = __pyx_v_end;
/* "csamtools.pyx":1945
* self.start = start
@@ -19765,7 +18741,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj
*
* def __next__(self):
*/
- __pyx_v_self->truncate = __pyx_v_truncate;
+ ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate = __pyx_v_truncate;
__pyx_r = 0;
goto __pyx_L0;
@@ -19774,24 +18750,12 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj
__Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_20IteratorColumnRegion_2__next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__;
-static PyObject *__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1947
* self.truncate = truncate
*
@@ -19800,7 +18764,10 @@ static PyObject *__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__(PyObject *
* """
*/
-static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_9csamtools_IteratorColumnRegion *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__;
+static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -19809,7 +18776,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1947);
/* "csamtools.pyx":1951
@@ -19829,7 +18796,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
* if self.n_plp < 0:
* raise ValueError("error during iteration" )
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
/* "csamtools.pyx":1953
* while 1:
@@ -19838,7 +18805,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
* raise ValueError("error during iteration" )
*
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
/* "csamtools.pyx":1954
@@ -19853,9 +18820,9 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
/* "csamtools.pyx":1956
* raise ValueError("error during iteration" )
@@ -19864,7 +18831,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
* raise StopIteration
*
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.plp == NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp == NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":1957
@@ -19876,9 +18843,9 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
/* "csamtools.pyx":1959
* raise StopIteration
@@ -19887,7 +18854,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
* if self.start < self.pos: continue
* if self.pos >= self.end: raise StopIteration
*/
- if (__pyx_v_self->truncate) {
+ if (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate) {
/* "csamtools.pyx":1960
*
@@ -19896,12 +18863,12 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
* if self.pos >= self.end: raise StopIteration
*
*/
- __pyx_t_1 = (__pyx_v_self->start < __pyx_v_self->__pyx_base.pos);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start < ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos);
if (__pyx_t_1) {
- goto __pyx_L3_continue;
- goto __pyx_L8;
+ goto __pyx_L5_continue;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
/* "csamtools.pyx":1961
* if self.truncate:
@@ -19910,16 +18877,16 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
*
* return makePileupProxy( &self.plp,
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.pos >= __pyx_v_self->end);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos >= ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->end);
if (__pyx_t_1) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L9;
+ goto __pyx_L11;
}
- __pyx_L9:;
- goto __pyx_L7;
+ __pyx_L11:;
+ goto __pyx_L9;
}
- __pyx_L7:;
+ __pyx_L9:;
/* "csamtools.pyx":1963
* if self.pos >= self.end: raise StopIteration
@@ -19937,12 +18904,12 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
*
* cdef class IteratorColumnAllRefs(IteratorColumn):
*/
- __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE [...]
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- __pyx_L3_continue:;
+ __pyx_L5_continue:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -19958,36 +18925,51 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_2__next__(struct __p
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":1972
+ * """
+ *
+ * def __cinit__(self, # <<<<<<<<<<<<<<
+ * Samfile samfile,
+ * **kwargs ):
+ */
+
+static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1972);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -20006,37 +18988,6 @@ static int __pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__py
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":1972
- * """
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * Samfile samfile,
- * **kwargs ):
- */
-
-static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- int __pyx_t_3;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__", 0);
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1972);
/* "csamtools.pyx":1977
*
@@ -20053,9 +19004,9 @@ static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_ob
if (__pyx_t_3) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":1980
*
@@ -20066,7 +19017,7 @@ static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_ob
*/
__pyx_t_4.__pyx_n = 1;
__pyx_t_4.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1980; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1980; __pyx_clineno = __LINE__; g [...]
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -20077,24 +19028,12 @@ static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_ob
__Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__;
-static PyObject *__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":1982
* self.setupIteratorData( self.tid, 0, max_pos, 1 )
*
@@ -20103,7 +19042,10 @@ static PyObject *__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject
* """
*/
-static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_9csamtools_IteratorColumnAllRefs *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__[] = "python version of next().\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__;
+static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -20115,7 +19057,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_RefNannySetupContext("__next__");
__Pyx_TraceCall("__next__", __pyx_f[0], 1982);
/* "csamtools.pyx":1986
@@ -20135,7 +19077,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
*
* if self.n_plp < 0:
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
/* "csamtools.pyx":1989
* self.cnext()
@@ -20144,7 +19086,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
* raise ValueError("error during iteration" )
*
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
/* "csamtools.pyx":1990
@@ -20159,9 +19101,9 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
/* "csamtools.pyx":1993
*
@@ -20170,7 +19112,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
* return makePileupProxy( &self.plp,
* self.tid,
*/
- __pyx_t_1 = (__pyx_v_self->__pyx_base.plp != NULL);
+ __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp != NULL);
if (__pyx_t_1) {
/* "csamtools.pyx":1994
@@ -20189,14 +19131,14 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
*
* # otherwise, proceed to next reference or stop
*/
- __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = [...]
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
/* "csamtools.pyx":2000
*
@@ -20205,7 +19147,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
* if self.tid < self.samfile.nreferences:
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
*/
- __pyx_v_self->__pyx_base.tid = (__pyx_v_self->__pyx_base.tid + 1);
+ ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid + 1);
/* "csamtools.pyx":2001
* # otherwise, proceed to next reference or stop
@@ -20214,9 +19156,9 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
* else:
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_self->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
@@ -20235,10 +19177,10 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
*/
__pyx_t_5.__pyx_n = 1;
__pyx_t_5.reopen = 0;
- __pyx_t_4 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_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*/ {
@@ -20252,7 +19194,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_2__next__(struct __
__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:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -20291,7 +19233,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
int __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_start", 0);
+ __Pyx_RefNannySetupContext("query_start");
__Pyx_TraceCall("query_start", __pyx_f[0], 2009);
/* "csamtools.pyx":2012
@@ -20473,7 +19415,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
int __pyx_t_3;
PyObject *__pyx_t_4 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_end", 0);
+ __Pyx_RefNannySetupContext("query_end");
__Pyx_TraceCall("query_end", __pyx_f[0], 2032);
/* "csamtools.pyx":2035
@@ -20680,7 +19622,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_seq_range", 0);
+ __Pyx_RefNannySetupContext("get_seq_range");
__Pyx_TraceCall("get_seq_range", __pyx_f[0], 2056);
/* "csamtools.pyx":2061
@@ -20808,7 +19750,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_qual_range", 0);
+ __Pyx_RefNannySetupContext("get_qual_range");
__Pyx_TraceCall("get_qual_range", __pyx_f[0], 2076);
/* "csamtools.pyx":2081
@@ -20913,20 +19855,6 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead___init__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2124
*
* # Now only called when instances are created from Python
@@ -20935,12 +19863,16 @@ static int __pyx_pw_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, P
* self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) )
*/
-static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 2124);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
/* "csamtools.pyx":2126
* def __init__(self):
@@ -20949,7 +19881,7 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtool
* # allocate some memory
* # If size is 0, calloc does not return a pointer that can be passed to free()
*/
- __pyx_v_self->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
/* "csamtools.pyx":2130
* # If size is 0, calloc does not return a pointer that can be passed to free()
@@ -20958,7 +19890,7 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtool
* self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
* self._delegate.data_len = 0
*/
- __pyx_v_self->_delegate->m_data = 40;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data = 40;
/* "csamtools.pyx":2131
* # so allocate 40 bytes for a new read
@@ -20967,7 +19899,7 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtool
* self._delegate.data_len = 0
*
*/
- __pyx_v_self->_delegate->data = ((uint8_t *)calloc(__pyx_v_self->_delegate->m_data, 1));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data = ((uint8_t *)calloc(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data, 1));
/* "csamtools.pyx":2132
* self._delegate.m_data = 40
@@ -20976,7 +19908,7 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtool
*
* def __dealloc__(self):
*/
- __pyx_v_self->_delegate->data_len = 0;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data_len = 0;
__pyx_r = 0;
__Pyx_TraceReturn(Py_None);
@@ -20984,15 +19916,6 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":2134
* self._delegate.data_len = 0
*
@@ -21001,10 +19924,11 @@ static void __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_sel
*
*/
-static void __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 2134);
/* "csamtools.pyx":2135
@@ -21014,25 +19938,12 @@ static void __pyx_pf_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_9csa
*
* def __str__(self):
*/
- bam_destroy1(__pyx_v_self->_delegate);
+ bam_destroy1(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_4__str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__;
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4__str__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2137
* bam_destroy1(self._delegate)
*
@@ -21041,7 +19952,10 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_se
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_2__str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
+struct wrapperbase __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__;
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_seq = NULL;
PyObject *__pyx_v_qual = NULL;
PyObject *__pyx_r = NULL;
@@ -21063,7 +19977,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 2137);
/* "csamtools.pyx":2149
@@ -21095,7 +20009,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* qual = self.qual
* else:
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_seq = __pyx_t_2;
__pyx_t_2 = 0;
@@ -21107,11 +20021,11 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* else:
* seq = self.seq.decode('ascii')
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
@@ -21122,7 +20036,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname,
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -21140,7 +20054,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* return "\t".join(map(str, (self.qname,
* self.flag,
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -21151,7 +20065,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2155
* seq = self.seq.decode('ascii')
@@ -21163,7 +20077,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_r);
__pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
/* "csamtools.pyx":2156
@@ -21173,7 +20087,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* self.rname,
* self.pos,
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
/* "csamtools.pyx":2157
@@ -21183,7 +20097,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* self.pos,
* self.mapq,
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
/* "csamtools.pyx":2158
@@ -21193,7 +20107,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* self.mapq,
* self.cigar,
*/
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
/* "csamtools.pyx":2159
@@ -21203,7 +20117,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* self.cigar,
* self.mrnm,
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
/* "csamtools.pyx":2160
@@ -21213,7 +20127,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* self.mrnm,
* self.mpos,
*/
- __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
/* "csamtools.pyx":2161
@@ -21223,7 +20137,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* self.mpos,
* self.rlen,
*/
- __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
/* "csamtools.pyx":2162
@@ -21233,7 +20147,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* self.rlen,
* seq,
*/
- __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
/* "csamtools.pyx":2163
@@ -21243,7 +20157,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
* seq,
* qual,
*/
- __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
/* "csamtools.pyx":2166
@@ -21253,10 +20167,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
*
* def compare(self, AlignedRead other):
*/
- __pyx_t_12 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__pyx_t_13 = PyTuple_New(12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_4);
@@ -21294,7 +20208,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
__pyx_t_11 = 0;
__pyx_t_12 = 0;
__pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_12));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_12, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -21305,7 +20219,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
__pyx_t_12 = PyTuple_New(1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_12));
PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_13);
__Pyx_GIVEREF(__pyx_t_13);
__pyx_t_13 = 0;
@@ -21343,23 +20257,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_6compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("compare (wrapper)", 0);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_6compare(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_other));
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2168
* self.tags )))
*
@@ -21368,7 +20265,9 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_se
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_other) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_3compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
int __pyx_v_retval;
bam1_t *__pyx_v_t;
bam1_t *__pyx_v_o;
@@ -21380,8 +20279,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("compare", 0);
+ __Pyx_RefNannySetupContext("compare");
__Pyx_TraceCall("compare", __pyx_f[0], 2168);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":2174
* cdef bam1_t *t, *o
@@ -21390,7 +20290,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs
* o = other._delegate
*
*/
- __pyx_v_t = __pyx_v_self->_delegate;
+ __pyx_v_t = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2175
*
@@ -21399,7 +20299,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs
*
* # uncomment for debugging purposes
*/
- __pyx_v_o = __pyx_v_other->_delegate;
+ __pyx_v_o = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_other)->_delegate;
/* "csamtools.pyx":2187
*
@@ -21422,9 +20322,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs
__Pyx_INCREF(__pyx_int_0);
__pyx_r = __pyx_int_0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2190
* return 0
@@ -21449,9 +20349,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":2193
*
@@ -21476,9 +20376,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
/* "csamtools.pyx":2195
* retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
@@ -21507,17 +20407,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6compare(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static Py_hash_t __pyx_pw_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self); /*proto*/
-static Py_hash_t __pyx_pw_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self) {
- Py_hash_t __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__hash__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8__hash__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2198
*
* # Disabled so long as __cmp__ is a special method
@@ -21526,11 +20415,12 @@ static Py_hash_t __pyx_pw_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_s
*
*/
-static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_self); /*proto*/
+static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_self) {
Py_hash_t __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__hash__", 0);
+ __Pyx_RefNannySetupContext("__hash__");
__Pyx_TraceCall("__hash__", __pyx_f[0], 2198);
/* "csamtools.pyx":2199
@@ -21551,17 +20441,6 @@ static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5qname___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2203
* property qname:
* """the query name (None if not present)"""
@@ -21570,7 +20449,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__p
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -21580,7 +20460,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2203);
/* "csamtools.pyx":2205
@@ -21590,7 +20470,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o
* if src.core.l_qname == 0: return None
* return _charptr_to_str(<char *>bam1_qname( src ))
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2206
* cdef bam1_t * src
@@ -21605,9 +20485,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2207
* src = self._delegate
@@ -21636,17 +20516,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2209
* return _charptr_to_str(<char *>bam1_qname( src ))
*
@@ -21655,7 +20524,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_s
* qname = _force_bytes(qname)
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname) {
+static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
bam1_t *__pyx_v_src;
int __pyx_v_l;
char *__pyx_v_p;
@@ -21671,7 +20541,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2209);
__Pyx_INCREF(__pyx_v_qname);
@@ -21696,9 +20566,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9c
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2211
* def __set__(self, qname ):
@@ -21720,7 +20590,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9c
* p = bam1_qname( src )
*
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2217
*
@@ -21791,17 +20661,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2259
*
* """
@@ -21810,7 +20669,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__p
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self) {
uint32_t *__pyx_v_cigar_p;
bam1_t *__pyx_v_src;
PyObject *__pyx_v_op = 0;
@@ -21827,7 +20687,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2259);
/* "csamtools.pyx":2265
@@ -21837,7 +20697,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o
* if src.core.n_cigar == 0: return None
*
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2266
*
@@ -21852,9 +20712,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2268
* if src.core.n_cigar == 0: return None
@@ -21864,7 +20724,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o
* for k from 0 <= k < src.core.n_cigar:
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_cigar = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -21921,7 +20781,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o
*
*/
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_op);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_op);
__Pyx_GIVEREF(__pyx_v_op);
@@ -21963,17 +20823,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_values));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2276
* return cigar
*
@@ -21982,7 +20831,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_s
* cdef uint32_t * p
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values) {
+static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
uint32_t *__pyx_v_p;
bam1_t *__pyx_v_src;
PyObject *__pyx_v_op = 0;
@@ -22006,7 +20856,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2276);
/* "csamtools.pyx":2277
@@ -22030,9 +20880,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2283
* cdef int k
@@ -22050,7 +20900,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c
*
* # get location of cigar string
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2288
*
@@ -22114,10 +20964,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c
__pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
__pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
__pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
} else {
@@ -22159,19 +21009,19 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
- index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
+ index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_8);
- index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_op);
__pyx_v_op = __pyx_t_8;
@@ -22234,17 +21084,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2316
* Returns the empty string if not present.
* '''
@@ -22253,7 +21092,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObje
* if c == None: return ""
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_v_c = NULL;
PyObject *__pyx_v_x = NULL;
PyObject *__pyx_v_y = NULL;
@@ -22275,7 +21115,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2316);
/* "csamtools.pyx":2317
@@ -22285,7 +21125,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
* if c == None: return ""
* else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_c = __pyx_t_1;
__pyx_t_1 = 0;
@@ -22306,7 +21146,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
__Pyx_INCREF(((PyObject *)__pyx_kp_s_16));
__pyx_r = ((PyObject *)__pyx_kp_s_16);
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
@@ -22321,7 +21161,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
if (PyList_CheckExact(__pyx_v_c) || PyTuple_CheckExact(__pyx_v_c)) {
__pyx_t_4 = __pyx_v_c; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
@@ -22331,10 +21171,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
__pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) {
+ if (PyList_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
__pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) {
+ } else if (PyTuple_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
__pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
} else {
@@ -22376,19 +21216,19 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
- index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
+ index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_8);
- index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_x);
__pyx_v_x = __pyx_t_8;
@@ -22400,7 +21240,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
__pyx_t_7 = PyInt_FromLong((__pyx_v_9csamtools_CODE2CIGAR[__pyx_t_12])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_y);
@@ -22415,7 +21255,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
@@ -22428,7 +21268,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
__pyx_t_3 = 0;
goto __pyx_L0;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -22452,17 +21292,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(struct
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_cigar));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2321
* else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
*
@@ -22471,7 +21300,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__
* parts = CIGAR_REGEX.findall( cigar )
*/
-static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar) {
+static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) {
PyObject *__pyx_v_parts = NULL;
PyObject *__pyx_v_x = NULL;
PyObject *__pyx_v_y = NULL;
@@ -22493,7 +21323,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2321);
/* "csamtools.pyx":2322
@@ -22516,12 +21346,12 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
}
if (__pyx_t_5) {
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2323
* def __set__(self, cigar):
@@ -22536,7 +21366,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_cigar);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_cigar);
__Pyx_GIVEREF(__pyx_v_cigar);
@@ -22555,7 +21385,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
* property seq:
*/
__pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
if (PyList_CheckExact(__pyx_v_parts) || PyTuple_CheckExact(__pyx_v_parts)) {
__pyx_t_1 = __pyx_v_parts; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
__pyx_t_8 = NULL;
@@ -22565,10 +21395,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
__pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) {
+ if (PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
__pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
- } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) {
+ } else if (PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
__pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
} else {
@@ -22610,19 +21440,19 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
+ index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L6_unpacking_failed;
+ index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_x);
__pyx_v_x = __pyx_t_9;
@@ -22633,7 +21463,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
__pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR2CODE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
__Pyx_INCREF(__pyx_v_x);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_x);
__Pyx_GIVEREF(__pyx_v_x);
@@ -22645,7 +21475,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_INCREF(__pyx_v_y);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_y);
__Pyx_GIVEREF(__pyx_v_y);
@@ -22653,7 +21483,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_6);
@@ -22664,7 +21494,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_r = 0;
@@ -22687,17 +21517,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3seq___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2330
*
* In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
@@ -22706,7 +21525,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx
* cdef char * s
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -22716,7 +21536,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2330);
/* "csamtools.pyx":2333
@@ -22726,7 +21546,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2335
* src = self._delegate
@@ -22741,9 +21561,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2337
* if src.core.l_qseq == 0: return None
@@ -22772,17 +21592,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_seq));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2339
* return get_seq_range(src, 0, src.core.l_qseq)
*
@@ -22791,7 +21600,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_sel
* # if no quality information is present, the first byte says 0xff.
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq) {
+static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_p;
char *__pyx_v_s;
@@ -22813,7 +21623,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2339);
__Pyx_INCREF(__pyx_v_seq);
@@ -22838,9 +21648,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2344
*
@@ -22862,7 +21672,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa
*
* l = len(seq)
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2352
* src = self._delegate
@@ -23002,17 +21812,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qual___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2384
*
* In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
@@ -23021,7 +21820,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__py
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -23031,7 +21831,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2384);
/* "csamtools.pyx":2389
@@ -23041,7 +21841,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2391
* src = self._delegate
@@ -23056,9 +21856,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2393
* if src.core.l_qseq == 0: return None
@@ -23087,17 +21887,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2395
* return get_qual_range(src, 0, src.core.l_qseq)
*
@@ -23106,7 +21895,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_se
* cdef bam1_t * src
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
+static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_p;
char *__pyx_v_q;
@@ -23127,7 +21917,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2395);
__Pyx_INCREF(__pyx_v_qual);
@@ -23138,7 +21928,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs
* p = bam1_qual( src )
* if qual == None or len(qual) == 0:
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2403
*
@@ -23187,9 +21977,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs
*/
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2408
* p[0] = 0xff
@@ -23246,7 +22036,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs
__pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
@@ -23257,7 +22047,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
@@ -23267,9 +22057,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L6;
}
- __pyx_L4:;
+ __pyx_L6:;
/* "csamtools.pyx":2415
* if src.core.l_qseq != l:
@@ -23320,17 +22110,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5query___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2431
* were not considered for alignment may have been retained."""
*
@@ -23339,7 +22118,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5query_1__get__(PyObject *__p
* cdef uint32_t start, end
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
@@ -23352,7 +22132,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2431);
/* "csamtools.pyx":2436
@@ -23362,7 +22142,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2438
* src = self._delegate
@@ -23377,9 +22157,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2440
* if src.core.l_qseq == 0: return None
@@ -23428,17 +22208,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2449
*
* In Python 3, this property is of type bytes."""
@@ -23447,7 +22216,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__p
* cdef uint32_t start, end
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
@@ -23460,7 +22230,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2449);
/* "csamtools.pyx":2453
@@ -23470,7 +22240,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_o
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2455
* src = self._delegate
@@ -23485,9 +22255,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_o
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2457
* if src.core.l_qseq == 0: return None
@@ -23536,17 +22306,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2464
* property qstart:
* """start index of the aligned query portion of the sequence (0-based, inclusive)"""
@@ -23555,7 +22314,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -23564,7 +22324,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2464);
/* "csamtools.pyx":2465
@@ -23575,7 +22335,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_
* property qend:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_start(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_query_start(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
@@ -23595,17 +22355,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qend___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2469
* property qend:
* """end index of the aligned query portion of the sequence (0-based, exclusive)"""
@@ -23614,7 +22363,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -23623,7 +22373,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2469);
/* "csamtools.pyx":2470
@@ -23634,7 +22384,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_ob
* property qlen:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_end(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_query_end(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
@@ -23654,17 +22404,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2474
* property qlen:
* """Length of the aligned query sequence"""
@@ -23673,7 +22412,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__py
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -23684,7 +22424,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2474);
/* "csamtools.pyx":2476
@@ -23694,7 +22434,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_ob
* return query_end(src)-query_start(src)
*
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2477
* cdef bam1_t * src
@@ -23725,17 +22465,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tags___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2494
* multiple times.
* """
@@ -23744,7 +22473,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__py
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_s;
char __pyx_v_auxtag[3];
@@ -23773,7 +22503,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2494);
/* "csamtools.pyx":2503
@@ -23783,7 +22513,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* if src.l_aux == 0: return []
* s = bam1_aux( src )
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2504
*
@@ -23796,13 +22526,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2505
* src = self._delegate
@@ -23821,7 +22551,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* while s < (src.data + src.data_len):
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_result = __pyx_t_2;
__pyx_t_2 = 0;
@@ -23920,7 +22650,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* value = <int>bam_aux2i(s)
*/
__pyx_v_s = (__pyx_v_s + 1);
- goto __pyx_L6;
+ goto __pyx_L8;
}
/* "csamtools.pyx":2517
@@ -23962,7 +22692,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* value = <int32_t>bam_aux2i(s)
*/
__pyx_v_s = (__pyx_v_s + 2);
- goto __pyx_L6;
+ goto __pyx_L8;
}
/* "csamtools.pyx":2520
@@ -24004,7 +22734,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* value = <float>bam_aux2f(s)
*/
__pyx_v_s = (__pyx_v_s + 4);
- goto __pyx_L6;
+ goto __pyx_L8;
}
/* "csamtools.pyx":2523
@@ -24038,7 +22768,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* value = <double>bam_aux2d(s)
*/
__pyx_v_s = (__pyx_v_s + 4);
- goto __pyx_L6;
+ goto __pyx_L8;
}
/* "csamtools.pyx":2526
@@ -24072,7 +22802,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* value = "%c" % <char>bam_aux2A(s)
*/
__pyx_v_s = (__pyx_v_s + 8);
- goto __pyx_L6;
+ goto __pyx_L8;
}
/* "csamtools.pyx":2529
@@ -24109,7 +22839,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* value = _charptr_to_str(<char*>bam_aux2Z(s))
*/
__pyx_v_s = (__pyx_v_s + 1);
- goto __pyx_L6;
+ goto __pyx_L8;
}
/* "csamtools.pyx":2532
@@ -24152,7 +22882,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
*/
__pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_s = (__pyx_v_s + (__pyx_t_7 + 1));
- goto __pyx_L6;
+ goto __pyx_L8;
}
/* "csamtools.pyx":2536
@@ -24214,21 +22944,21 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
- index = 0; __pyx_t_2 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
+ index = 0; __pyx_t_2 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L9_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 1; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L7_unpacking_failed;
+ index = 1; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L9_unpacking_failed;
__Pyx_GOTREF(__pyx_t_8);
- index = 2; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed;
+ index = 2; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L9_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L8_unpacking_done;
- __pyx_L7_unpacking_failed:;
+ goto __pyx_L10_unpacking_done;
+ __pyx_L9_unpacking_failed:;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L8_unpacking_done:;
+ __pyx_L10_unpacking_done:;
}
__pyx_t_12 = __Pyx_PyInt_from_py_uint8_t(__pyx_t_2); if (unlikely((__pyx_t_12 == (uint8_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -24248,9 +22978,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
* s += 1
*/
__pyx_v_s = (__pyx_v_s + ((5 + (__pyx_v_nvalues * __pyx_v_byte_size)) - 1));
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
/* "csamtools.pyx":2542
* s += 5 + ( nvalues * byte_size) - 1
@@ -24268,11 +22998,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
*
* return result
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_value);
@@ -24314,17 +23046,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tags));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2548
* return result
*
@@ -24333,7 +23054,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_se
* cdef uint8_t * s
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags) {
+static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_s;
char *__pyx_v_temp;
@@ -24375,7 +23097,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2548);
/* "csamtools.pyx":2554
@@ -24385,7 +23107,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
*
* fmts, args = ["<"], []
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2556
* src = self._delegate
@@ -24395,12 +23117,12 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
* if tags != None:
*/
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_138));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_138));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_138));
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_fmts = __pyx_t_1;
__pyx_t_1 = 0;
__pyx_v_args = __pyx_t_2;
@@ -24435,10 +23157,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_5 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
__pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
- } else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_2)) {
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
__pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
} else {
@@ -24480,19 +23202,19 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L6_unpacking_failed;
+ index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_6);
- index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L6_unpacking_failed;
+ index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L7_unpacking_done;
- __pyx_L6_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L7_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_pytag);
__pyx_v_pytag = __pyx_t_6;
@@ -24527,9 +23249,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_DECREF(__pyx_v_pytag);
__pyx_v_pytag = __pyx_t_7;
__pyx_t_7 = 0;
- goto __pyx_L8;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
/* "csamtools.pyx":2564
* if not type(pytag) is bytes:
@@ -24599,7 +23321,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_datatype);
__pyx_v_datatype = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L10;
+ goto __pyx_L12;
}
/*else*/ {
@@ -24611,7 +23333,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
* # signed ints
*/
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
@@ -24619,7 +23341,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
@@ -24697,7 +23419,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_datatype);
__pyx_v_datatype = __pyx_t_6;
__pyx_t_6 = 0;
- goto __pyx_L12;
+ goto __pyx_L14;
}
/* "csamtools.pyx":2578
@@ -24722,7 +23444,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_datatype);
__pyx_v_datatype = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L12;
+ goto __pyx_L14;
}
/* "csamtools.pyx":2579
@@ -24740,7 +23462,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -24750,7 +23472,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L12;
+ goto __pyx_L14;
}
/*else*/ {
@@ -24772,8 +23494,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_v_datatype = __pyx_t_6;
__pyx_t_6 = 0;
}
- __pyx_L12:;
- goto __pyx_L11;
+ __pyx_L14:;
+ goto __pyx_L13;
}
/*else*/ {
@@ -24799,7 +23521,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_datatype);
__pyx_v_datatype = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L13;
+ goto __pyx_L15;
}
/* "csamtools.pyx":2585
@@ -24824,7 +23546,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_datatype);
__pyx_v_datatype = __pyx_t_6;
__pyx_t_6 = 0;
- goto __pyx_L13;
+ goto __pyx_L15;
}
/* "csamtools.pyx":2586
@@ -24842,7 +23564,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
__pyx_t_6 = 0;
@@ -24852,7 +23574,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L13;
+ goto __pyx_L15;
}
/*else*/ {
@@ -24874,11 +23596,11 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_v_datatype = __pyx_t_1;
__pyx_t_1 = 0;
}
- __pyx_L13:;
+ __pyx_L15:;
}
- __pyx_L11:;
+ __pyx_L13:;
}
- __pyx_L10:;
+ __pyx_L12:;
/* "csamtools.pyx":2589
* else: datafmt, datatype = "I", 'I'
@@ -24891,7 +23613,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_1 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_datafmt);
@@ -24962,7 +23684,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_7 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__pyx_t_14 = PyList_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
PyList_SET_ITEM(__pyx_t_14, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
PyList_SET_ITEM(__pyx_t_14, 1, __pyx_t_8);
@@ -24976,7 +23698,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_13 = 0;
__pyx_t_7 = 0;
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
@@ -24988,7 +23710,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
@@ -25005,6 +23727,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
* continue
*
*/
+ if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_datafmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":2595
@@ -25014,10 +23739,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
*
* if t is float:
*/
- goto __pyx_L4_continue;
- goto __pyx_L9;
+ goto __pyx_L6_continue;
+ goto __pyx_L11;
}
- __pyx_L9:;
+ __pyx_L11:;
/* "csamtools.pyx":2597
* continue
@@ -25046,7 +23771,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = __pyx_t_13;
__pyx_t_13 = 0;
- goto __pyx_L14;
+ goto __pyx_L16;
}
/* "csamtools.pyx":2599
@@ -25094,7 +23819,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = __pyx_t_7;
__pyx_t_7 = 0;
- goto __pyx_L16;
+ goto __pyx_L18;
}
/* "csamtools.pyx":2603
@@ -25119,7 +23844,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = __pyx_t_13;
__pyx_t_13 = 0;
- goto __pyx_L16;
+ goto __pyx_L18;
}
/* "csamtools.pyx":2604
@@ -25137,7 +23862,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_13 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_13));
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_13));
__Pyx_GIVEREF(((PyObject *)__pyx_t_13));
__pyx_t_13 = 0;
@@ -25147,7 +23872,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_Raise(__pyx_t_13, 0, 0, 0);
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ goto __pyx_L18;
}
/*else*/ {
@@ -25169,8 +23894,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_v_pytype = __pyx_t_7;
__pyx_t_7 = 0;
}
- __pyx_L16:;
- goto __pyx_L15;
+ __pyx_L18:;
+ goto __pyx_L17;
}
/*else*/ {
@@ -25196,7 +23921,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = __pyx_t_13;
__pyx_t_13 = 0;
- goto __pyx_L17;
+ goto __pyx_L19;
}
/* "csamtools.pyx":2609
@@ -25221,7 +23946,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = __pyx_t_7;
__pyx_t_7 = 0;
- goto __pyx_L17;
+ goto __pyx_L19;
}
/* "csamtools.pyx":2610
@@ -25239,7 +23964,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
@@ -25249,7 +23974,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L17;
+ goto __pyx_L19;
}
/*else*/ {
@@ -25271,10 +23996,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_v_pytype = __pyx_t_13;
__pyx_t_13 = 0;
}
- __pyx_L17:;
+ __pyx_L19:;
}
- __pyx_L15:;
- goto __pyx_L14;
+ __pyx_L17:;
+ goto __pyx_L16;
}
/*else*/ {
@@ -25303,9 +24028,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_DECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_7;
__pyx_t_7 = 0;
- goto __pyx_L18;
+ goto __pyx_L20;
}
- __pyx_L18:;
+ __pyx_L20:;
/* "csamtools.pyx":2616
* if t is not bytes:
@@ -25335,7 +24060,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = __pyx_t_13;
__pyx_t_13 = 0;
- goto __pyx_L19;
+ goto __pyx_L21;
}
/*else*/ {
@@ -25361,9 +24086,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_v_pytype = __pyx_t_13;
__pyx_t_13 = 0;
}
- __pyx_L19:;
+ __pyx_L21:;
}
- __pyx_L14:;
+ __pyx_L16:;
/* "csamtools.pyx":2621
* fmt, pytype = "2sc%is" % (len(value)+1), 'Z'
@@ -25398,7 +24123,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
* fmts.append( fmt )
*/
__pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_14);
@@ -25409,7 +24134,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_7 = 0;
__pyx_t_14 = 0;
__pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -25426,8 +24151,11 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
*
* fmt = "".join(fmts)
*/
+ if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_fmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L4_continue:;
+ __pyx_L6_continue:;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -25441,7 +24169,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_v_fmts));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fmts));
__Pyx_GIVEREF(((PyObject *)__pyx_v_fmts));
@@ -25466,7 +24194,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
__Pyx_INCREF(__pyx_v_fmt);
PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_fmt);
__Pyx_GIVEREF(__pyx_v_fmt);
@@ -25490,7 +24218,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_GOTREF(__pyx_t_14);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_total_size);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_total_size);
__Pyx_GIVEREF(__pyx_v_total_size);
@@ -25522,7 +24250,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
* *args )
*/
__pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fmt);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fmt);
__Pyx_GIVEREF(__pyx_v_fmt);
@@ -25551,19 +24279,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
-
- /* "csamtools.pyx":2640
- * pysam_bam_update( src,
- * src.l_aux,
- * total_size, # <<<<<<<<<<<<<<
- * bam1_aux( src ) )
- *
- */
- if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5:;
+ if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":2641
* src.l_aux,
@@ -25605,6 +24324,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
* # check if there is direct path from buffer.raw to tmp
*/
__pyx_v_s = bam1_aux(__pyx_v_src);
+ if (unlikely(!__pyx_v_buffer)) { __Pyx_RaiseUnboundLocalError("buffer"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_14 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":2652
*
@@ -25613,8 +24333,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
* memcpy( s, temp, total_size )
*
*/
- if (unlikely(!__pyx_v_buffer)) { __Pyx_RaiseUnboundLocalError("buffer"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_14 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
__pyx_t_18 = PyBytes_AsString(__pyx_t_14); if (unlikely((!__pyx_t_18) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
@@ -25629,9 +24347,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
*/
__pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
memcpy(__pyx_v_s, __pyx_v_temp, __pyx_t_16);
- goto __pyx_L20;
+ goto __pyx_L22;
}
- __pyx_L20:;
+ __pyx_L22:;
__pyx_r = 0;
goto __pyx_L0;
@@ -25665,17 +24383,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4flag___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2657
* property flag:
* """properties flag"""
@@ -25684,7 +24391,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25692,10 +24400,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2657);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25714,17 +24422,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_flag));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2658
* """properties flag"""
* def __get__(self): return self._delegate.core.flag
@@ -25733,7 +24430,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_se
* property rname:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag) {
+static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
@@ -25741,10 +24439,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2658);
__pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_flag); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.flag = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -25757,17 +24455,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rname___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2676
*
* """
@@ -25776,7 +24463,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__p
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25784,10 +24472,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2676);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25806,17 +24494,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2677
* """
* def __get__(self): return self._delegate.core.tid
@@ -25825,7 +24502,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_s
* property tid:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
+static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -25833,10 +24511,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2677);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.tid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -25849,17 +24527,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3tid___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2690
*
* """
@@ -25868,7 +24535,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25876,10 +24544,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2690);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25898,17 +24566,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2691
* """
* def __get__(self): return self._delegate.core.tid
@@ -25917,7 +24574,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_sel
* property pos:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
+static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -25925,10 +24583,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2691);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.tid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -25941,17 +24599,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3pos___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2695
* property pos:
* """0-based leftmost coordinate"""
@@ -25960,7 +24607,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx
* ## setting the cigar string also updates the "bin" attribute
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25968,10 +24616,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2695);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25990,17 +24638,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_pos));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2696
* """0-based leftmost coordinate"""
* def __get__(self): return self._delegate.core.pos
@@ -26009,7 +24646,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_sel
* cdef bam1_t * src
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos) {
+static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
bam1_t *__pyx_v_src;
int __pyx_r;
__Pyx_RefNannyDeclarations
@@ -26018,7 +24656,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2696);
/* "csamtools.pyx":2699
@@ -26028,7 +24666,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csa
* if src.core.n_cigar:
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2700
* cdef bam1_t * src
@@ -26047,7 +24685,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csa
* src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
*/
__pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)));
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
@@ -26060,7 +24698,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csa
*/
__pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, (__pyx_v_src->core.pos + 1));
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2704
* else:
@@ -26070,7 +24708,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csa
* """properties bin"""
*/
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_pos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.pos = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -26083,17 +24721,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3bin___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2707
* property bin:
* """properties bin"""
@@ -26102,7 +24729,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx
* property rlen:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26110,10 +24738,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2707);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26132,17 +24760,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_bin));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2708
* """properties bin"""
* def __get__(self): return self._delegate.core.bin
@@ -26151,7 +24768,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_sel
* '''length of the read (read only). Returns 0 if not given.'''
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin) {
+static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
@@ -26159,10 +24777,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2708);
__pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_bin); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.bin = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -26175,17 +24793,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2711
* property rlen:
* '''length of the read (read only). Returns 0 if not given.'''
@@ -26194,7 +24801,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__py
* '''aligned reference position of the read on the reference genome.
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26202,10 +24810,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2711);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26224,17 +24832,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4aend___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2717
* aend points to one past the last aligned residue.
* Returns None if not available.'''
@@ -26243,7 +24840,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__py
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -26256,7 +24854,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2717);
/* "csamtools.pyx":2719
@@ -26266,7 +24864,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_ob
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2720
* cdef bam1_t * src
@@ -26275,7 +24873,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_ob
* return None
* return bam_calend(&src.core, bam1_cigar(src))
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -26301,9 +24899,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_ob
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2722
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
@@ -26333,17 +24931,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4alen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2727
* '''aligned length of the read on the reference genome. Returns None if
* not available.'''
@@ -26352,7 +24939,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__py
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -26365,7 +24953,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2727);
/* "csamtools.pyx":2729
@@ -26375,7 +24963,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2730
* cdef bam1_t * src
@@ -26384,7 +24972,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob
* return None
* return bam_calend(&src.core,
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -26410,9 +24998,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2732
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
@@ -26430,7 +25018,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob
*
* property mapq:
*/
- __pyx_t_2 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - __pyx_v_self->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -26450,17 +25038,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2738
* property mapq:
* """mapping quality"""
@@ -26469,7 +25046,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26477,10 +25055,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2738);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26499,17 +25077,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2739
* """mapping quality"""
* def __get__(self): return self._delegate.core.qual
@@ -26518,7 +25085,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_se
* property mrnm:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
+static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
@@ -26526,10 +25094,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2739);
__pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_qual); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.qual = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -26542,17 +25110,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2745
* deprecated, use RNEXT instead.
* """
@@ -26561,7 +25118,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__py
* property rnext:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26569,10 +25127,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2745);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26591,17 +25149,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2746
* """
* def __get__(self): return self._delegate.core.mtid
@@ -26610,7 +25157,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_se
* """the :term:`reference` id of the mate """
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
+static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -26618,10 +25166,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2746);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -26634,17 +25182,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2749
* property rnext:
* """the :term:`reference` id of the mate """
@@ -26653,7 +25190,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__p
* property mpos:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26661,10 +25199,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2749);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26683,17 +25221,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2750
* """the :term:`reference` id of the mate """
* def __get__(self): return self._delegate.core.mtid
@@ -26702,7 +25229,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_s
* """the position of the mate
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
+static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -26710,10 +25238,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2750);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -26726,17 +25254,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2754
* """the position of the mate
* deprecated, use PNEXT instead."""
@@ -26745,7 +25262,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__py
* property pnext:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26753,10 +25271,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2754);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26775,17 +25293,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2755
* deprecated, use PNEXT instead."""
* def __get__(self): return self._delegate.core.mpos
@@ -26794,7 +25301,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_se
* """the position of the mate"""
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
+static int __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -26802,10 +25310,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2755);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -26818,17 +25326,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2758
* property pnext:
* """the position of the mate"""
@@ -26837,7 +25334,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__p
* property isize:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26845,10 +25343,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2758);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2758; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2758; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26867,17 +25365,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2759
* """the position of the mate"""
* def __get__(self): return self._delegate.core.mpos
@@ -26886,7 +25373,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_s
* """the insert size
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
+static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -26894,10 +25382,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2759);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -26910,17 +25398,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5isize___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2763
* """the insert size
* deprecated: use tlen instead"""
@@ -26929,7 +25406,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__p
* property tlen:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26937,10 +25415,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2763);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26959,17 +25437,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2764
* deprecated: use tlen instead"""
* def __get__(self): return self._delegate.core.isize
@@ -26978,7 +25445,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_s
* """the insert size"""
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
+static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -26986,10 +25454,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2764);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.isize = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -27002,17 +25470,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2767
* property tlen:
* """the insert size"""
@@ -27021,7 +25478,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__py
* property is_paired:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27029,10 +25487,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2767);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -27051,17 +25509,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2768
* """the insert size"""
* def __get__(self): return self._delegate.core.isize
@@ -27070,7 +25517,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_se
* """true if read is paired in sequencing"""
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
+static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -27078,10 +25526,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2768);
__pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->_delegate->core.isize = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -27094,17 +25542,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2771
* property is_paired:
* """true if read is paired in sequencing"""
@@ -27113,7 +25550,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject
* if val: self._delegate.core.flag |= BAM_FPAIRED
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27121,10 +25559,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2771);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong(((__pyx_v_self->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(((((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -27143,17 +25581,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(struct __p
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2772
* """true if read is paired in sequencing"""
* def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
@@ -27162,7 +25589,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx
* else: self._delegate.core.flag &= ~BAM_FPAIRED
*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -27170,7 +25598,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2772);
/* "csamtools.pyx":2773
@@ -27182,8 +25610,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 1);
+ goto __pyx_L5;
}
/*else*/ {
@@ -27194,9 +25622,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob
* property is_proper_pair:
* """true if read is mapped in a proper pair"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -27209,17 +25637,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2777
* property is_proper_pair:
* """true if read is mapped in a proper pair"""
@@ -27228,7 +25645,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyO
* if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27237,10 +25655,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(stru
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2777);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -27266,17 +25684,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(stru
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2778
* """true if read is mapped in a proper pair"""
* def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
@@ -27285,7 +25692,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject
* else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
*/
-static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -27293,7 +25701,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2778);
/* "csamtools.pyx":2779
@@ -27305,8 +25713,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 2);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 2);
+ goto __pyx_L5;
}
/*else*/ {
@@ -27317,9 +25725,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __
* property is_unmapped:
* """true if read itself is unmapped"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~2));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~2));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -27332,17 +25740,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2783
* property is_unmapped:
* """true if read itself is unmapped"""
@@ -27351,7 +25748,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObje
* if val: self._delegate.core.flag |= BAM_FUNMAP
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27360,10 +25758,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2783);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -27389,17 +25787,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(struct
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2784
* """true if read itself is unmapped"""
* def __get__(self): return (self.flag & BAM_FUNMAP) != 0
@@ -27408,7 +25795,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__
* else: self._delegate.core.flag &= ~BAM_FUNMAP
*/
-static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -27416,7 +25804,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2784);
/* "csamtools.pyx":2785
@@ -27428,8 +25816,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 4);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 4);
+ goto __pyx_L5;
}
/*else*/ {
@@ -27440,9 +25828,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx
* property mate_is_unmapped:
* """true if the mate is unmapped"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~4));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~4));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -27455,17 +25843,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2789
* property mate_is_unmapped:
* """true if the mate is unmapped"""
@@ -27474,7 +25851,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(P
* if val: self._delegate.core.flag |= BAM_FMUNMAP
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27483,10 +25861,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(st
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2789);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -27512,17 +25890,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(st
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2790
* """true if the mate is unmapped"""
* def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
@@ -27531,7 +25898,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObjec
* else: self._delegate.core.flag &= ~BAM_FMUNMAP
*/
-static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -27539,7 +25907,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2790);
/* "csamtools.pyx":2791
@@ -27551,8 +25919,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 8);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 8);
+ goto __pyx_L5;
}
/*else*/ {
@@ -27563,9 +25931,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct
* property is_reverse:
* """true if read is mapped to reverse strand"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~8));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~8));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -27578,17 +25946,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2795
* property is_reverse:
* """true if read is mapped to reverse strand"""
@@ -27597,7 +25954,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObjec
* if val: self._delegate.core.flag |= BAM_FREVERSE
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27606,10 +25964,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct _
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2795);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -27635,17 +25993,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(struct _
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2796
* """true if read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FREVERSE) != 0
@@ -27654,7 +26001,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__p
* else: self._delegate.core.flag &= ~BAM_FREVERSE
*/
-static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -27662,7 +26010,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2796);
/* "csamtools.pyx":2797
@@ -27674,8 +26022,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 16);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 16);
+ goto __pyx_L5;
}
/*else*/ {
@@ -27686,9 +26034,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_
* property mate_is_reverse:
* """true is read is mapped to reverse strand"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~16));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~16));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -27701,17 +26049,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2801
* property mate_is_reverse:
* """true is read is mapped to reverse strand"""
@@ -27720,7 +26057,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(Py
* if val: self._delegate.core.flag |= BAM_FMREVERSE
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27729,10 +26067,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(str
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2801);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_32); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -27758,17 +26096,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(str
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2802
* """true is read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
@@ -27777,7 +26104,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject
* else: self._delegate.core.flag &= ~BAM_FMREVERSE
*/
-static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -27785,7 +26113,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct _
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2802);
/* "csamtools.pyx":2803
@@ -27797,8 +26125,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct _
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 32);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 32);
+ goto __pyx_L5;
}
/*else*/ {
@@ -27809,9 +26137,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct _
* property is_read1:
* """true if this is read1"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~32));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~32));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -27824,17 +26152,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct _
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2807
* property is_read1:
* """true if this is read1"""
@@ -27843,7 +26160,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *
* if val: self._delegate.core.flag |= BAM_FREAD1
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27852,10 +26170,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2807);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_64); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -27881,17 +26199,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(struct __py
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2808
* """true if this is read1"""
* def __get__(self): return (self.flag & BAM_FREAD1) != 0
@@ -27900,7 +26207,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_
* else: self._delegate.core.flag &= ~BAM_FREAD1
*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -27908,7 +26216,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2808);
/* "csamtools.pyx":2809
@@ -27920,8 +26228,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 64);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 64);
+ goto __pyx_L5;
}
/*else*/ {
@@ -27932,9 +26240,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj
* property is_read2:
* """true if this is read2"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~64));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~64));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -27947,17 +26255,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2813
* property is_read2:
* """true if this is read2"""
@@ -27966,7 +26263,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *
* if val: self._delegate.core.flag |= BAM_FREAD2
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -27975,10 +26273,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2813);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_128); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -28004,17 +26302,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(struct __py
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2814
* """true if this is read2"""
* def __get__(self): return (self.flag & BAM_FREAD2) != 0
@@ -28023,7 +26310,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_
* else: self._delegate.core.flag &= ~BAM_FREAD2
*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -28031,7 +26319,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2814);
/* "csamtools.pyx":2815
@@ -28043,8 +26331,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 128);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 128);
+ goto __pyx_L5;
}
/*else*/ {
@@ -28055,9 +26343,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj
* property is_secondary:
* """true if not primary alignment"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~128));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~128));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -28070,17 +26358,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2819
* property is_secondary:
* """true if not primary alignment"""
@@ -28089,7 +26366,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObj
* if val: self._delegate.core.flag |= BAM_FSECONDARY
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28098,10 +26376,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2819);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_256); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -28127,17 +26405,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(struct
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2820
* """true if not primary alignment"""
* def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
@@ -28146,7 +26413,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *_
* else: self._delegate.core.flag &= ~BAM_FSECONDARY
*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -28154,7 +26422,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2820);
/* "csamtools.pyx":2821
@@ -28166,8 +26434,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __py
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 256);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 256);
+ goto __pyx_L5;
}
/*else*/ {
@@ -28178,9 +26446,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __py
* property is_qcfail:
* """true if QC failure"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~256));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~256));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -28193,17 +26461,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __py
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2825
* property is_qcfail:
* """true if QC failure"""
@@ -28212,7 +26469,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject
* if val: self._delegate.core.flag |= BAM_FQCFAIL
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28221,10 +26479,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2825);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_512); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -28250,17 +26508,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(struct __p
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2826
* """true if QC failure"""
* def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
@@ -28269,7 +26516,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx
* else: self._delegate.core.flag &= ~BAM_FQCFAIL
*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -28277,7 +26525,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2826);
/* "csamtools.pyx":2827
@@ -28289,8 +26537,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 512);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 512);
+ goto __pyx_L5;
}
/*else*/ {
@@ -28301,9 +26549,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob
* property is_duplicate:
* """true if optical or PCR duplicate"""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~512));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~512));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -28316,17 +26564,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2831
* property is_duplicate:
* """true if optical or PCR duplicate"""
@@ -28335,7 +26572,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObj
* if val: self._delegate.core.flag |= BAM_FDUP
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28344,10 +26582,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2831);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_1024); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -28373,17 +26611,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(struct
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2832
* """true if optical or PCR duplicate"""
* def __get__(self): return (self.flag & BAM_FDUP) != 0
@@ -28392,7 +26619,8 @@ static int __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *_
* else: self._delegate.core.flag &= ~BAM_FDUP
*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -28400,7 +26628,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 2832);
/* "csamtools.pyx":2833
@@ -28412,8 +26640,8 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __py
*/
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1024);
- goto __pyx_L3;
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 1024);
+ goto __pyx_L5;
}
/*else*/ {
@@ -28424,9 +26652,9 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __py
* property positions:
* """a list of reference positions that this read aligns to."""
*/
- __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1024));
+ ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1024));
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = 0;
goto __pyx_L0;
@@ -28439,17 +26667,6 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __py
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_9positions___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2837
* property positions:
* """a list of reference positions that this read aligns to."""
@@ -28458,7 +26675,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(PyObject
* cdef int op
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self) {
uint32_t __pyx_v_k;
uint32_t __pyx_v_i;
uint32_t __pyx_v_pos;
@@ -28479,7 +26697,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2837);
/* "csamtools.pyx":2843
@@ -28489,7 +26707,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p
* if src.core.n_cigar == 0: return []
*
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2844
*
@@ -28502,13 +26720,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p
if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2846
* if src.core.n_cigar == 0: return []
@@ -28518,7 +26736,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p
* cigar_p = bam1_cigar(src)
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_result = __pyx_t_2;
__pyx_t_2 = 0;
@@ -28605,14 +26823,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_6 = PyList_Append(__pyx_v_result, __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
- goto __pyx_L6;
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
/* "csamtools.pyx":2857
* result.append( i )
@@ -28673,17 +26894,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(struct __p
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2867
* Unaligned position are marked by None.
* """
@@ -28692,7 +26902,8 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyOb
* cdef int op
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self) {
uint32_t __pyx_v_k;
uint32_t __pyx_v_i;
uint32_t __pyx_v_pos;
@@ -28715,7 +26926,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 2867);
/* "csamtools.pyx":2873
@@ -28725,7 +26936,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
* if src.core.n_cigar == 0: return []
*
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2874
*
@@ -28738,13 +26949,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2876
* if src.core.n_cigar == 0: return []
@@ -28754,7 +26965,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
* qpos = 0
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_v_result = __pyx_t_2;
__pyx_t_2 = 0;
@@ -28858,12 +27069,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
* qpos += 1
* pos += l
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
@@ -28932,10 +27146,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
* qpos += 1
*
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(Py_None);
@@ -28989,10 +27206,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
* pos += l
*
*/
+ if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_t_2, 0, Py_None);
__Pyx_GIVEREF(Py_None);
@@ -29051,29 +27271,58 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(struc
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_10overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n ";
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":2904
+ *
+ *
+ * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
+ * """return number of aligned bases of read overlapping the interval *start* and *end*
+ * on the reference sequence.
+ */
+
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_5overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n ";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
- PyObject *__pyx_r = 0;
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_pos;
+ uint32_t __pyx_v_overlap;
+ int __pyx_v_op;
+ int __pyx_v_o;
+ uint32_t *__pyx_v_cigar_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_l = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("overlap (wrapper)", 0);
+ int __pyx_t_1;
+ uint32_t __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ uint32_t __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ uint32_t __pyx_t_8;
+ uint32_t __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("overlap");
+ __Pyx_TraceCall("overlap", __pyx_f[0], 2904);
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
if (likely(values[0])) kw_args--;
@@ -29086,7 +27335,7 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_s
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -29105,46 +27354,6 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_s
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_10overlap(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), __pyx_v_start, __pyx_v_end);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":2904
- *
- *
- * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
- * """return number of aligned bases of read overlapping the interval *start* and *end*
- * on the reference sequence.
- */
-
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
- uint32_t __pyx_v_k;
- uint32_t __pyx_v_pos;
- uint32_t __pyx_v_overlap;
- int __pyx_v_op;
- int __pyx_v_o;
- uint32_t *__pyx_v_cigar_p;
- bam1_t *__pyx_v_src;
- PyObject *__pyx_v_l = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- int __pyx_t_1;
- uint32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- uint32_t __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- uint32_t __pyx_t_8;
- uint32_t __pyx_t_9;
- int __pyx_t_10;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("overlap", 0);
- __Pyx_TraceCall("overlap", __pyx_f[0], 2904);
/* "csamtools.pyx":2913
* cdef bam1_t * src
@@ -29162,7 +27371,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c
* if src.core.n_cigar == 0: return 0
* pos = src.core.pos
*/
- __pyx_v_src = __pyx_v_self->_delegate;
+ __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
/* "csamtools.pyx":2916
*
@@ -29177,9 +27386,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c
__Pyx_INCREF(__pyx_int_0);
__pyx_r = __pyx_int_0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":2917
* src = self._delegate
@@ -29307,12 +27516,12 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c
__pyx_t_1 = (__pyx_v_o > 0);
if (__pyx_t_1) {
__pyx_v_overlap = (__pyx_v_overlap + __pyx_v_o);
- goto __pyx_L7;
+ goto __pyx_L10;
}
- __pyx_L7:;
- goto __pyx_L6;
+ __pyx_L10:;
+ goto __pyx_L9;
}
- __pyx_L6:;
+ __pyx_L9:;
/* "csamtools.pyx":2929
* if o > 0: overlap += o
@@ -29376,18 +27585,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_9c
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_12opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("opt (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_12opt(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tag));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2934
* return overlap
*
@@ -29396,12 +27593,14 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self,
* #see bam_aux.c: bam_aux_get() and bam_aux2i() etc
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_6opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
uint8_t *__pyx_v_v;
- CYTHON_UNUSED int __pyx_v_nvalues;
+ int __pyx_v_nvalues;
PyObject *__pyx_v_btag = NULL;
PyObject *__pyx_v_auxtype = NULL;
- CYTHON_UNUSED PyObject *__pyx_v_bytesize = NULL;
+ PyObject *__pyx_v_bytesize = NULL;
PyObject *__pyx_v_values = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -29422,7 +27621,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("opt", 0);
+ __Pyx_RefNannySetupContext("opt");
__Pyx_TraceCall("opt", __pyx_f[0], 2934);
/* "csamtools.pyx":2939
@@ -29445,7 +27644,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
* auxtype = chr(v[0])
*/
__pyx_t_2 = PyBytes_AsString(((PyObject *)__pyx_v_btag)); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_v = bam_aux_get(__pyx_v_self->_delegate, __pyx_t_2);
+ __pyx_v_v = bam_aux_get(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate, __pyx_t_2);
/* "csamtools.pyx":2941
* btag = _force_bytes(tag)
@@ -29459,7 +27658,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_148), __pyx_v_tag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -29469,9 +27668,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":2942
* v = bam_aux_get(self._delegate, btag)
@@ -29483,7 +27682,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((__pyx_v_v[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -29534,7 +27733,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/* "csamtools.pyx":2945
@@ -29566,7 +27765,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/* "csamtools.pyx":2947
@@ -29598,7 +27797,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/* "csamtools.pyx":2949
@@ -29630,7 +27829,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/* "csamtools.pyx":2951
@@ -29659,7 +27858,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_r = ((PyObject *)__pyx_t_4);
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/* "csamtools.pyx":2955
@@ -29685,7 +27884,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/* "csamtools.pyx":2957
@@ -29738,21 +27937,21 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed;
+ index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L5_unpacking_failed;
+ index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L5_unpacking_failed;
+ index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L6_unpacking_done;
- __pyx_L5_unpacking_failed:;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L6_unpacking_done:;
+ __pyx_L8_unpacking_done:;
}
__pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
@@ -29773,7 +27972,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__Pyx_INCREF(__pyx_v_values);
__pyx_r = __pyx_v_values;
goto __pyx_L0;
- goto __pyx_L4;
+ goto __pyx_L6;
}
/*else*/ {
@@ -29787,7 +27986,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_149), __pyx_v_auxtype); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
@@ -29798,7 +27997,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L4:;
+ __pyx_L6:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -29821,18 +28020,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12opt(struct __pyx_obj_9csamt
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_14fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
-static PyObject *__pyx_pw_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("fancy_str (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11AlignedRead_14fancy_str(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":2964
*
*
@@ -29841,7 +28028,9 @@ static PyObject *__pyx_pw_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v
* """
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_11AlignedRead_7fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
+static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_v_ret_string = NULL;
PyObject *__pyx_v_field_names = NULL;
PyObject *__pyx_v_fields_names_in_order = NULL;
@@ -29863,7 +28052,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fancy_str", 0);
+ __Pyx_RefNannySetupContext("fancy_str");
__Pyx_TraceCall("fancy_str", __pyx_f[0], 2964);
/* "csamtools.pyx":2967
@@ -29874,7 +28063,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* "tid": "Contig index",
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_ret_string = __pyx_t_1;
__pyx_t_1 = 0;
@@ -29916,7 +28105,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
*/
__pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_n_s__tid));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tid));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__tid));
@@ -29981,6 +28170,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* if not f in self.__dict__:
* continue
*/
+ if (unlikely(((PyObject *)__pyx_v_fields_names_in_order) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_1 = ((PyObject *)__pyx_v_fields_names_in_order); __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
for (;;) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
@@ -29996,7 +28188,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* continue
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = ((PySequence_Contains(__pyx_t_3, __pyx_v_f))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -30010,10 +28202,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*
*/
- goto __pyx_L3_continue;
- goto __pyx_L5;
+ goto __pyx_L5_continue;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
/* "csamtools.pyx":2995
* if not f in self.__dict__:
@@ -30022,6 +28214,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
*
* for f in self.__dict__:
*/
+ if (unlikely(((PyObject *)__pyx_v_ret_string) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_3 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_field_names), __pyx_v_f); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_kp_s_169), __pyx_v_f); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -30029,10 +28224,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
__pyx_t_7 = PyNumber_Add(__pyx_t_6, ((PyObject *)__pyx_kp_s_170)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
@@ -30041,7 +28236,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
@@ -30056,7 +28251,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_L3_continue:;
+ __pyx_L5_continue:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -30067,7 +28262,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* if not f in field_names:
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_9 = __pyx_t_1; __Pyx_INCREF(__pyx_t_9); __pyx_t_2 = 0;
@@ -30079,10 +28274,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_9)) {
+ if (PyList_CheckExact(__pyx_t_9)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_9)) break;
__pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
- } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_9)) {
+ } else if (PyTuple_CheckExact(__pyx_t_9)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
__pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
} else {
@@ -30107,6 +28302,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
* return ret_string
*/
+ if (unlikely(((PyObject *)__pyx_v_field_names) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__pyx_t_5 = ((PyDict_Contains(((PyObject *)__pyx_v_field_names), __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (!__pyx_t_5);
if (__pyx_t_4) {
@@ -30118,10 +28316,13 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
* return ret_string
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_ret_string) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
@@ -30130,7 +28331,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
@@ -30145,9 +28346,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L8;
+ goto __pyx_L10;
}
- __pyx_L8:;
+ __pyx_L10:;
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
@@ -30185,20 +28386,6 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- __pyx_r = __pyx_pf_9csamtools_11PileupProxy___init__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3019
* will change.
* '''
@@ -30207,7 +28394,8 @@ static int __pyx_pw_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, P
*
*/
-static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30215,8 +28403,11 @@ static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 3019);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
/* "csamtools.pyx":3020
* '''
@@ -30243,17 +28434,6 @@ static int __pyx_pf_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11PileupProxy_2__str__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3022
* raise TypeError("This class cannot be instantiated from Python")
*
@@ -30262,7 +28442,8 @@ static PyObject *__pyx_pw_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_se
* "\n" +\
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30274,7 +28455,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9cs
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 3022);
/* "csamtools.pyx":3023
@@ -30303,14 +28484,14 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9cs
* "\n" +\
* "\n".join( map(str, self.pileups) )
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
@@ -30321,7 +28502,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9cs
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -30332,7 +28513,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9cs
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
@@ -30353,10 +28534,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9cs
*/
__pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -30367,7 +28548,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9cs
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -30400,17 +28581,6 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_9cs
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11PileupProxy_3tid___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3029
* property tid:
* '''the chromosome ID as is defined in the header'''
@@ -30419,7 +28589,8 @@ static PyObject *__pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx
* property n:
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30427,10 +28598,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3029);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -30449,17 +28620,6 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11PileupProxy_1n___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3033
* property n:
* '''number of reads mapping to this column.'''
@@ -30468,7 +28628,8 @@ static PyObject *__pyx_pw_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v
*
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30476,10 +28637,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3033);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -30498,17 +28659,6 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_9
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
-static int __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self), ((PyObject *)__pyx_v_n));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3034
* '''number of reads mapping to this column.'''
* def __get__(self): return self.n_pu
@@ -30517,7 +28667,8 @@ static int __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self,
* property pos:
*/
-static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n) {
+static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
+static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -30525,10 +28676,10 @@ static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamt
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_RefNannySetupContext("__set__");
__Pyx_TraceCall("__set__", __pyx_f[0], 3034);
__pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_n); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->n_pu = __pyx_t_1;
+ ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
@@ -30541,17 +28692,6 @@ static int __pyx_pf_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_9csamt
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11PileupProxy_3pos___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3037
*
* property pos:
@@ -30560,7 +28700,8 @@ static PyObject *__pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx
* property pileups:
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30568,10 +28709,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3037);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3037; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3037; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -30590,17 +28731,6 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3041
* property pileups:
* '''list of reads (:class:`pysam.PileupRead`) aligned to this column'''
@@ -30609,7 +28739,8 @@ static PyObject *__pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *_
* pileups = []
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self) {
int __pyx_v_x;
PyObject *__pyx_v_pileups = NULL;
PyObject *__pyx_r = NULL;
@@ -30622,7 +28753,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3041);
/* "csamtools.pyx":3043
@@ -30633,7 +28764,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx
* if self.plp[0] == NULL:
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_pileups = __pyx_t_1;
__pyx_t_1 = 0;
@@ -30644,7 +28775,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx
* raise ValueError("PileupProxy accessed after iterator finished")
*
*/
- __pyx_t_2 = ((__pyx_v_self->plp[0]) == NULL);
+ __pyx_t_2 = ((((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[0]) == NULL);
if (__pyx_t_2) {
/* "csamtools.pyx":3046
@@ -30659,9 +28790,9 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
/* "csamtools.pyx":3050
* # warning: there could be problems if self.n and self.buf are
@@ -30670,7 +28801,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx
* pileups.append( makePileupRead( &(self.plp[0][x])) )
* return pileups
*/
- __pyx_t_3 = __pyx_v_self->n_pu;
+ __pyx_t_3 = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
/* "csamtools.pyx":3051
@@ -30680,7 +28811,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx
* return pileups
*
*/
- __pyx_t_1 = __pyx_f_9csamtools_makePileupRead((&((__pyx_v_self->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_pileups) == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_1 = __pyx_f_9csamtools_makePileupRead((&((((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -30712,20 +28846,6 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
- __pyx_r = __pyx_pf_9csamtools_10PileupRead___init__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3058
* '''
*
@@ -30734,7 +28854,8 @@ static int __pyx_pw_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, Py
*
*/
-static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30742,8 +28863,11 @@ static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_RefNannySetupContext("__init__");
__Pyx_TraceCall("__init__", __pyx_f[0], 3058);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
/* "csamtools.pyx":3059
*
@@ -30770,17 +28894,6 @@ static int __pyx_pf_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_2__str__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3061
* raise TypeError("This class cannot be instantiated from Python")
*
@@ -30789,7 +28902,8 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_sel
*
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30805,7 +28919,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 3061);
/* "csamtools.pyx":3062
@@ -30818,22 +28932,22 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csa
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_9 = PyTuple_New(7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3);
@@ -30856,7 +28970,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csa
__pyx_t_7 = 0;
__pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -30867,7 +28981,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csa
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
@@ -30900,17 +29014,6 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_2__str__(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_9alignment___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3066
* property alignment:
* """a :class:`pysam.AlignedRead` object of the aligned read"""
@@ -30919,11 +29022,12 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(PyObject *
* property qpos:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3066);
/* "csamtools.pyx":3067
@@ -30934,8 +29038,8 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __py
* """position of the read base at the pileup site, 0-based"""
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->_alignment));
- __pyx_r = ((PyObject *)__pyx_v_self->_alignment);
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment));
+ __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -30946,17 +29050,6 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(struct __py
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_4qpos___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3070
* property qpos:
* """position of the read base at the pileup site, 0-based"""
@@ -30965,7 +29058,8 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx
* property indel:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -30973,7 +29067,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3070);
/* "csamtools.pyx":3071
@@ -30984,7 +29078,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj
* """indel length; 0 for no indel, positive for ins and negative for del"""
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31003,17 +29097,6 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_5indel___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3074
* property indel:
* """indel length; 0 for no indel, positive for ins and negative for del"""
@@ -31022,7 +29105,8 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_5indel_1__get__(PyObject *__py
* property is_del:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31030,7 +29114,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3074);
/* "csamtools.pyx":3075
@@ -31041,7 +29125,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_ob
* """1 iff the base on the padded read is a deletion"""
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3075; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3075; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31060,17 +29144,6 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_6is_del___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3078
* property is_del:
* """1 iff the base on the padded read is a deletion"""
@@ -31079,7 +29152,8 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__p
* property is_head:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31087,7 +29161,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_o
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3078);
/* "csamtools.pyx":3079
@@ -31098,7 +29172,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_o
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31117,17 +29191,6 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(struct __pyx_o
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_7is_head___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3081
* return self._is_del
* property is_head:
@@ -31136,7 +29199,8 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__
* property is_tail:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31144,7 +29208,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3081);
/* "csamtools.pyx":3082
@@ -31155,7 +29219,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31174,17 +29238,6 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(struct __pyx_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3084
* return self._is_head
* property is_tail:
@@ -31193,7 +29246,8 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__
* property level:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31201,7 +29255,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3084);
/* "csamtools.pyx":3085
@@ -31212,7 +29266,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31231,17 +29285,6 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_10PileupRead_5level___get__(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3087
* return self._is_tail
* property level:
@@ -31250,7 +29293,8 @@ static PyObject *__pyx_pw_9csamtools_10PileupRead_5level_1__get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_9csamtools_PileupRead *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31258,7 +29302,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_ob
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3087);
/* "csamtools.pyx":3088
@@ -31269,7 +29313,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_ob
* class Outs:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31288,32 +29332,44 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(struct __pyx_ob
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+/* "csamtools.pyx":3092
+ * class Outs:
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1): # <<<<<<<<<<<<<<
+ * self.streams = []
+ * self.id = id
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_9csamtools_4Outs___init__[] = "Outs.__init__(self, id=1)";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_9csamtools_4Outs_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs___init__)};
-static PyObject *__pyx_pw_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyMethodDef __pyx_mdef_9csamtools_4Outs___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_4Outs___init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs___init__)};
+static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_id = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__");
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3092);
__pyx_self = __pyx_self;
{
PyObject* values[2] = {0,0};
- values[1] = ((PyObject *)((PyObject *)__pyx_int_1));
+ values[1] = ((PyObject *)__pyx_int_1);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
if (likely(values[0])) kw_args--;
@@ -31325,7 +29381,7 @@ static PyObject *__pyx_pw_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObj
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -31346,29 +29402,6 @@ static PyObject *__pyx_pw_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObj
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_4Outs___init__(__pyx_self, __pyx_v_self, __pyx_v_id);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":3092
- * class Outs:
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1): # <<<<<<<<<<<<<<
- * self.streams = []
- * self.id = id
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
- __Pyx_TraceCall("__init__", __pyx_f[0], 3092);
/* "csamtools.pyx":3093
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
@@ -31378,7 +29411,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__py
*
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__streams, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -31404,31 +29437,46 @@ static PyObject *__pyx_pf_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__py
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_2setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_3setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pw_9csamtools_4Outs_3setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_2setdevice)};
-static PyObject *__pyx_pw_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3096
+ * self.id = id
+ *
+ * def setdevice(self, filename): # <<<<<<<<<<<<<<
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY)
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_1setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_1setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pf_9csamtools_4Outs_1setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_1setdevice)};
+static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_fd = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("setdevice (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setdevice");
+ __Pyx_TraceCall("setdevice", __pyx_f[0], 3096);
__pyx_self = __pyx_self;
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
if (likely(values[0])) kw_args--;
@@ -31441,7 +29489,7 @@ static PyObject *__pyx_pw_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyOb
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -31460,32 +29508,6 @@ static PyObject *__pyx_pw_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyOb
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_4Outs_2setdevice(__pyx_self, __pyx_v_self, __pyx_v_filename);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":3096
- * self.id = id
- *
- * def setdevice(self, filename): # <<<<<<<<<<<<<<
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY)
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
- PyObject *__pyx_v_fd = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setdevice", 0);
- __Pyx_TraceCall("setdevice", __pyx_f[0], 3096);
/* "csamtools.pyx":3098
* def setdevice(self, filename):
@@ -31505,7 +29527,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
@@ -31529,7 +29551,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__
__pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
@@ -31555,31 +29577,47 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_4setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_5setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pw_9csamtools_4Outs_5setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_4setfile)};
-static PyObject *__pyx_pw_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3101
+ * self.setfd(fd)
+ *
+ * def setfile(self, filename): # <<<<<<<<<<<<<<
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_2setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_2setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pf_9csamtools_4Outs_2setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_2setfile)};
+static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_fd = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("setfile (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setfile");
+ __Pyx_TraceCall("setfile", __pyx_f[0], 3101);
__pyx_self = __pyx_self;
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
if (likely(values[0])) kw_args--;
@@ -31592,7 +29630,7 @@ static PyObject *__pyx_pw_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObje
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -31611,33 +29649,6 @@ static PyObject *__pyx_pw_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObje
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_4Outs_4setfile(__pyx_self, __pyx_v_self, __pyx_v_filename);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":3101
- * self.setfd(fd)
- *
- * def setfile(self, filename): # <<<<<<<<<<<<<<
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
- PyObject *__pyx_v_fd = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfile", 0);
- __Pyx_TraceCall("setfile", __pyx_f[0], 3101);
/* "csamtools.pyx":3103
* def setfile(self, filename):
@@ -31666,7 +29677,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__py
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
@@ -31693,7 +29704,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__py
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
@@ -31720,31 +29731,46 @@ static PyObject *__pyx_pf_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__py
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_6setfd[] = "Outs.setfd(self, fd)";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_7setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pw_9csamtools_4Outs_7setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_6setfd)};
-static PyObject *__pyx_pw_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3106
+ * self.setfd(fd)
+ *
+ * def setfd(self, fd): # <<<<<<<<<<<<<<
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd)
+ */
+
+static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_3setfd[] = "Outs.setfd(self, fd)";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_3setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pf_9csamtools_4Outs_3setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_3setfd)};
+static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_fd = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_ofd = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("setfd (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setfd");
+ __Pyx_TraceCall("setfd", __pyx_f[0], 3106);
__pyx_self = __pyx_self;
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
if (likely(values[0])) kw_args--;
@@ -31757,7 +29783,7 @@ static PyObject *__pyx_pw_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -31776,32 +29802,6 @@ static PyObject *__pyx_pw_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools_4Outs_6setfd(__pyx_self, __pyx_v_self, __pyx_v_fd);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":3106
- * self.setfd(fd)
- *
- * def setfd(self, fd): # <<<<<<<<<<<<<<
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd)
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd) {
- PyObject *__pyx_v_ofd = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfd", 0);
- __Pyx_TraceCall("setfd", __pyx_f[0], 3106);
/* "csamtools.pyx":3107
*
@@ -31818,7 +29818,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -31898,7 +29898,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_
__pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
@@ -31924,7 +29924,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
@@ -31950,20 +29950,6 @@ static PyObject *__pyx_pf_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_8restore[] = "Outs.restore(self)\nrestore previous output stream";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_9restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pw_9csamtools_4Outs_9restore, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_8restore)};
-static PyObject *__pyx_pw_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("restore (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_9csamtools_4Outs_8restore(__pyx_self, ((PyObject *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3114
* os.close(fd) # Close other unit (look out, caller.)
*
@@ -31972,7 +29958,10 @@ static PyObject *__pyx_pw_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObje
* if self.streams:
*/
-static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_9csamtools_4Outs_4restore[] = "Outs.restore(self)\nrestore previous output stream";
+static PyMethodDef __pyx_mdef_9csamtools_4Outs_4restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pf_9csamtools_4Outs_4restore, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_4restore)};
+static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31984,8 +29973,9 @@ static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("restore", 0);
+ __Pyx_RefNannySetupContext("restore");
__Pyx_TraceCall("restore", __pyx_f[0], 3114);
+ __pyx_self = __pyx_self;
/* "csamtools.pyx":3116
* def restore(self):
@@ -32060,7 +30050,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__py
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
@@ -32091,7 +30081,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__py
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
@@ -32112,9 +30102,9 @@ static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__py
__Pyx_GOTREF(__pyx_t_3);
if (__Pyx_DelItemInt(__pyx_t_3, -1, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -32132,18 +30122,65 @@ static PyObject *__pyx_pf_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__py
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+/* "csamtools.pyx":3125
+ * del self.streams[-1]
+ *
+ * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
+ * args = (),
+ * catch_stdout = True ):
+ */
+
+static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static char __pyx_doc_9csamtools__samtools_dispatch[] = "_samtools_dispatch(method, args=(), catch_stdout=True)\ncall ``method`` in samtools providing arguments in args.\n \n .. note:: \n This method redirects stdout to capture it \n from samtools. If for some reason stdout disappears\n the reason might be in this method.\n\n .. note::\n The current implementation might only work on linux.\n\n .. note::\n This method captures stdout and stderr us [...]
-static PyMethodDef __pyx_mdef_9csamtools_1_samtools_dispatch = {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pw_9csamtools_1_samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools__samtools_dispatch)};
-static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyMethodDef __pyx_mdef_9csamtools__samtools_dispatch = {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pf_9csamtools__samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools__samtools_dispatch)};
+static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_method = 0;
PyObject *__pyx_v_args = 0;
PyObject *__pyx_v_catch_stdout = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,0};
- PyObject *__pyx_r = 0;
+ PyObject *__pyx_v_stderr_h = NULL;
+ PyObject *__pyx_v_stderr_f = NULL;
+ PyObject *__pyx_v_stdout_h = NULL;
+ PyObject *__pyx_v_stdout_f = NULL;
+ PyObject *__pyx_v_stdout_save = NULL;
+ char **__pyx_v_cargs;
+ int __pyx_v_i;
+ int __pyx_v_n;
+ int __pyx_v_retval;
+ PyObject *__pyx_v_inf = NULL;
+ PyObject *__pyx_v_out_stdout = NULL;
+ PyObject *__pyx_v_out_stderr = NULL;
+ PyObject *__pyx_v_a = NULL;
+ PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("_samtools_dispatch (wrapper)", 0);
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *(*__pyx_t_7)(PyObject *);
+ int __pyx_t_8;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ PyObject *(*__pyx_t_13)(PyObject *);
+ char *__pyx_t_14;
+ PyObject *__pyx_t_15 = NULL;
+ PyObject *__pyx_t_16 = NULL;
+ PyObject *__pyx_t_17 = NULL;
+ PyObject *__pyx_t_18 = NULL;
+ PyObject *__pyx_t_19 = NULL;
+ PyObject *__pyx_t_20 = NULL;
+ PyObject *__pyx_t_21 = NULL;
+ PyObject *__pyx_t_22 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_samtools_dispatch");
+ __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3125);
__pyx_self = __pyx_self;
{
PyObject* values[3] = {0,0,0};
@@ -32159,8 +30196,7 @@ static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, P
values[2] = __pyx_k_176;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
@@ -32168,7 +30204,7 @@ static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, P
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__method);
if (likely(values[0])) kw_args--;
@@ -32185,7 +30221,7 @@ static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, P
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -32208,63 +30244,6 @@ static PyObject *__pyx_pw_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, P
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_9csamtools__samtools_dispatch(__pyx_self, __pyx_v_method, __pyx_v_args, __pyx_v_catch_stdout);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":3125
- * del self.streams[-1]
- *
- * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
- * args = (),
- * catch_stdout = True ):
- */
-
-static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout) {
- PyObject *__pyx_v_stderr_h = NULL;
- PyObject *__pyx_v_stderr_f = NULL;
- PyObject *__pyx_v_stdout_h = NULL;
- PyObject *__pyx_v_stdout_f = NULL;
- PyObject *__pyx_v_stdout_save = NULL;
- char **__pyx_v_cargs;
- int __pyx_v_i;
- int __pyx_v_n;
- int __pyx_v_retval;
- PyObject *__pyx_v_inf = NULL;
- PyObject *__pyx_v_out_stdout = NULL;
- PyObject *__pyx_v_out_stderr = NULL;
- PyObject *__pyx_v_a = NULL;
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- PyObject *(*__pyx_t_7)(PyObject *);
- int __pyx_t_8;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- Py_ssize_t __pyx_t_12;
- PyObject *(*__pyx_t_13)(PyObject *);
- char *__pyx_t_14;
- PyObject *__pyx_t_15 = NULL;
- PyObject *__pyx_t_16 = NULL;
- PyObject *__pyx_t_17 = NULL;
- PyObject *__pyx_t_18 = NULL;
- PyObject *__pyx_t_19 = NULL;
- PyObject *__pyx_t_20 = NULL;
- PyObject *__pyx_t_21 = NULL;
- PyObject *__pyx_t_22 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_samtools_dispatch", 0);
- __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3125);
__Pyx_INCREF(__pyx_v_method);
__Pyx_INCREF(__pyx_v_args);
__Pyx_INCREF(__pyx_v_catch_stdout);
@@ -32297,7 +30276,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
@@ -32323,7 +30302,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
@@ -32333,12 +30312,12 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L4;
+ goto __pyx_L7;
}
- __pyx_L4:;
- goto __pyx_L3;
+ __pyx_L7:;
+ goto __pyx_L6;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":3156
*
@@ -32383,19 +30362,19 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
+ index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
- index = 1; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L5_unpacking_failed;
+ index = 1; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L6_unpacking_done;
- __pyx_L5_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L6_unpacking_done:;
+ __pyx_L9_unpacking_done:;
}
__pyx_v_stderr_h = __pyx_t_3;
__pyx_t_3 = 0;
@@ -32465,19 +30444,19 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed;
+ index = 0; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L11_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed;
+ index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L11_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L9_unpacking_done;
- __pyx_L8_unpacking_failed:;
+ goto __pyx_L12_unpacking_done;
+ __pyx_L11_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L9_unpacking_done:;
+ __pyx_L12_unpacking_done:;
}
__pyx_v_stdout_h = __pyx_t_2;
__pyx_t_2 = 0;
@@ -32505,25 +30484,25 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* stdout_save.setfd( stdout_h )
* except AttributeError:
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -32537,14 +30516,14 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* except AttributeError:
* # stdout has already been redirected
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_INCREF(__pyx_v_stdout_h);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_h);
__Pyx_GIVEREF(__pyx_v_stdout_h);
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -32553,8 +30532,8 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L17_try_end;
- __pyx_L10_error:;
+ goto __pyx_L20_try_end;
+ __pyx_L13_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -32570,7 +30549,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_AttributeError);
if (__pyx_t_8) {
__Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_3);
__Pyx_GOTREF(__pyx_t_2);
@@ -32582,7 +30561,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
*
* # patch for `samtools view`
*/
- __pyx_t_6 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3166; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_6 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3166; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_v_catch_stdout);
__pyx_v_catch_stdout = __pyx_t_6;
@@ -32590,20 +30569,20 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L11_exception_handled;
+ goto __pyx_L14_exception_handled;
}
- __pyx_L12_except_error:;
+ __pyx_L15_except_error:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
goto __pyx_L1_error;
- __pyx_L11_exception_handled:;
+ __pyx_L14_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
- __pyx_L17_try_end:;
+ __pyx_L20_try_end:;
}
/* "csamtools.pyx":3171
@@ -32630,9 +30609,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L21;
+ goto __pyx_L24;
}
- __pyx_L21:;
+ __pyx_L24:;
/* "csamtools.pyx":3173
* if method == "view":
@@ -32642,7 +30621,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* # do the function call to samtools
*/
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_178));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_178));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_178));
@@ -32655,12 +30634,12 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_DECREF(__pyx_v_args);
__pyx_v_args = __pyx_t_3;
__pyx_t_3 = 0;
- goto __pyx_L20;
+ goto __pyx_L23;
}
- __pyx_L20:;
- goto __pyx_L7;
+ __pyx_L23:;
+ goto __pyx_L10;
}
- __pyx_L7:;
+ __pyx_L10:;
/* "csamtools.pyx":3179
* cdef int i, n, retval
@@ -32693,7 +30672,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* # allocate two more for first (dummy) argument (contains command)
*/
__pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
if (PyList_CheckExact(__pyx_v_args) || PyTuple_CheckExact(__pyx_v_args)) {
__pyx_t_2 = __pyx_v_args; __Pyx_INCREF(__pyx_t_2); __pyx_t_12 = 0;
__pyx_t_13 = NULL;
@@ -32703,10 +30682,10 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__pyx_t_13 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_13 && PyList_CheckExact(__pyx_t_2)) {
+ if (PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_2)) break;
__pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
- } else if (!__pyx_t_13 && PyTuple_CheckExact(__pyx_t_2)) {
+ } else if (PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
__pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
} else {
@@ -32805,6 +30784,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
*/
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
+ if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_3 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":3195
* # needs to be before reading back the file contents
@@ -32813,8 +30793,6 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* try:
* with open( stdout_f, "r") as inf:
*/
- if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -32843,26 +30821,25 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* except UnicodeDecodeError:
*/
/*with:*/ {
- if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;} }
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;} }__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_stdout_f);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__r));
PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____enter__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____enter__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L38_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L38_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
@@ -32870,9 +30847,8 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_18);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_4);
- __pyx_v_inf = __pyx_t_4;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_inf = __pyx_t_3;
+ __pyx_t_3 = 0;
/* "csamtools.pyx":3198
* try:
@@ -32881,23 +30857,23 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf:
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L44_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_v_out_stdout = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L44_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_v_out_stdout = __pyx_t_2;
+ __pyx_t_2 = 0;
}
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
- goto __pyx_L48_try_end;
- __pyx_L41_error:;
+ goto __pyx_L51_try_end;
+ __pyx_L44_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "csamtools.pyx":3197
* stdout_save.restore()
@@ -32908,86 +30884,86 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
*/
/*except:*/ {
__Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_3, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_3);
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_INCREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
__pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
__Pyx_GOTREF(__pyx_t_19);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
__pyx_t_1 = (!__pyx_t_5);
if (__pyx_t_1) {
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_3);
__Pyx_GIVEREF(__pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_2);
- __Pyx_ErrRestore(__pyx_t_3, __pyx_t_4, __pyx_t_2);
- __pyx_t_3 = 0; __pyx_t_4 = 0; __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
- goto __pyx_L52;
+ __Pyx_ErrRestore(__pyx_t_2, __pyx_t_3, __pyx_t_4);
+ __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_4 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ goto __pyx_L54;
}
- __pyx_L52:;
+ __pyx_L54:;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L42_exception_handled;
+ goto __pyx_L45_exception_handled;
}
- __pyx_L43_except_error:;
+ __pyx_L46_except_error:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- goto __pyx_L27_error;
- __pyx_L42_exception_handled:;
+ goto __pyx_L30_error;
+ __pyx_L45_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- __pyx_L48_try_end:;
+ __pyx_L51_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
__pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_181, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
__Pyx_GOTREF(__pyx_t_18);
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
}
}
- goto __pyx_L53;
- __pyx_L35_error:;
+ goto __pyx_L55;
+ __pyx_L38_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L27_error;
- __pyx_L53:;
+ goto __pyx_L30_error;
+ __pyx_L55:;
}
}
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L34_try_end;
- __pyx_L27_error:;
+ goto __pyx_L37_try_end;
+ __pyx_L30_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "csamtools.pyx":3199
* with open( stdout_f, "r") as inf:
@@ -32999,10 +30975,10 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
if (__pyx_t_8) {
__Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_2);
/* "csamtools.pyx":3200
* out_stdout = inf.readlines()
@@ -33012,25 +30988,25 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* out_stdout = inf.read()
*/
/*with:*/ {
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_stdout_f);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L58_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_21 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L58_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_18, &__pyx_t_17, &__pyx_t_16);
@@ -33038,10 +31014,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_21);
__Pyx_XDECREF(__pyx_v_inf);
- __pyx_v_inf = __pyx_t_21;
- __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __pyx_v_inf = __pyx_t_20;
+ __pyx_t_20 = 0;
/* "csamtools.pyx":3202
* with open( stdout_f, "rb") as inf:
@@ -33050,23 +31025,22 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* os.remove( stdout_f )
* else:
*/
- __pyx_t_21 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
+ __pyx_t_20 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L64_error;}
__Pyx_GOTREF(__pyx_t_20);
- __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L64_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XDECREF(__pyx_v_out_stdout);
- __pyx_v_out_stdout = __pyx_t_20;
- __pyx_t_20 = 0;
+ __pyx_v_out_stdout = __pyx_t_6;
+ __pyx_t_6 = 0;
}
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
- goto __pyx_L69_try_end;
- __pyx_L62_error:;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ goto __pyx_L71_try_end;
+ __pyx_L64_error:;
__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
/* "csamtools.pyx":3200
* out_stdout = inf.readlines()
@@ -33077,93 +31051,93 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
*/
/*except:*/ {
__Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_20, &__pyx_t_21, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_20, &__pyx_t_21) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_20);
__Pyx_GOTREF(__pyx_t_21);
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_22));
+ __Pyx_INCREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_20);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_20);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_20);
__Pyx_GIVEREF(__pyx_t_20);
__Pyx_INCREF(__pyx_t_21);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_21);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_21);
__Pyx_GIVEREF(__pyx_t_21);
- __Pyx_INCREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
__pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_22, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
__Pyx_GOTREF(__pyx_t_19);
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
__pyx_t_5 = (!__pyx_t_1);
if (__pyx_t_5) {
+ __Pyx_GIVEREF(__pyx_t_6);
__Pyx_GIVEREF(__pyx_t_20);
__Pyx_GIVEREF(__pyx_t_21);
- __Pyx_GIVEREF(__pyx_t_6);
- __Pyx_ErrRestore(__pyx_t_20, __pyx_t_21, __pyx_t_6);
- __pyx_t_20 = 0; __pyx_t_21 = 0; __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
- goto __pyx_L73;
+ __Pyx_ErrRestore(__pyx_t_6, __pyx_t_20, __pyx_t_21);
+ __pyx_t_6 = 0; __pyx_t_20 = 0; __pyx_t_21 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ goto __pyx_L74;
}
- __pyx_L73:;
+ __pyx_L74:;
__Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L63_exception_handled;
+ goto __pyx_L65_exception_handled;
}
- __pyx_L64_except_error:;
+ __pyx_L66_except_error:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- goto __pyx_L29_except_error;
- __pyx_L63_exception_handled:;
+ goto __pyx_L32_except_error;
+ __pyx_L65_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- __pyx_L69_try_end:;
+ __pyx_L71_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
__pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_182, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
}
}
- goto __pyx_L74;
- __pyx_L56_error:;
+ goto __pyx_L75;
+ __pyx_L58_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L29_except_error;
- __pyx_L74:;
+ goto __pyx_L32_except_error;
+ __pyx_L75:;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L28_exception_handled;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ goto __pyx_L31_exception_handled;
}
- __pyx_L29_except_error:;
+ __pyx_L32_except_error:;
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
goto __pyx_L1_error;
- __pyx_L28_exception_handled:;
+ __pyx_L31_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
- __pyx_L34_try_end:;
+ __pyx_L37_try_end:;
}
/* "csamtools.pyx":3203
@@ -33173,22 +31147,22 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* else:
* out_stdout = []
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__remove); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__remove); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
- __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L26;
+ goto __pyx_L29;
}
/*else*/ {
@@ -33199,12 +31173,12 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
*
* # get error messages
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_v_out_stdout = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_v_out_stdout = ((PyObject *)__pyx_t_4);
+ __pyx_t_4 = 0;
}
- __pyx_L26:;
+ __pyx_L29:;
/* "csamtools.pyx":3208
*
@@ -33237,25 +31211,25 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* except UnicodeDecodeError:
*/
/*with:*/ {
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_stderr_f);
__Pyx_GIVEREF(__pyx_v_stderr_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____enter__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L83_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L83_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s____enter__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L84_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L84_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
@@ -33263,10 +31237,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_18);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_v_inf);
- __pyx_v_inf = __pyx_t_4;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_inf = __pyx_t_2;
+ __pyx_t_2 = 0;
/* "csamtools.pyx":3211
* try:
@@ -33275,26 +31248,26 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf:
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L89_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L90_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L90_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L89_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_v_out_stderr = __pyx_t_3;
- __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_out_stderr = __pyx_t_4;
+ __pyx_t_4 = 0;
}
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
- goto __pyx_L96_try_end;
- __pyx_L89_error:;
+ goto __pyx_L97_try_end;
+ __pyx_L90_error:;
__Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "csamtools.pyx":3210
* pysam_unset_stderr()
@@ -33305,74 +31278,74 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
*/
/*except:*/ {
__Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_2, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_INCREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_21 = PyTuple_New(3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_21));
__Pyx_INCREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
__Pyx_INCREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_21, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
+ __Pyx_INCREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_21, 2, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_21, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
__Pyx_GOTREF(__pyx_t_19);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
__pyx_t_1 = (!__pyx_t_5);
if (__pyx_t_1) {
- __Pyx_GIVEREF(__pyx_t_3);
__Pyx_GIVEREF(__pyx_t_4);
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_ErrRestore(__pyx_t_3, __pyx_t_4, __pyx_t_2);
- __pyx_t_3 = 0; __pyx_t_4 = 0; __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L91_except_error;}
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_ErrRestore(__pyx_t_4, __pyx_t_2, __pyx_t_3);
+ __pyx_t_4 = 0; __pyx_t_2 = 0; __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
goto __pyx_L100;
}
__pyx_L100:;
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L90_exception_handled;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L91_exception_handled;
}
- __pyx_L91_except_error:;
+ __pyx_L92_except_error:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- goto __pyx_L75_error;
- __pyx_L90_exception_handled:;
+ goto __pyx_L76_error;
+ __pyx_L91_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- __pyx_L96_try_end:;
+ __pyx_L97_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
__pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_183, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
__Pyx_GOTREF(__pyx_t_18);
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L75_error;}
+ if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
}
}
goto __pyx_L101;
- __pyx_L83_error:;
+ __pyx_L84_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L75_error;
+ goto __pyx_L76_error;
__pyx_L101:;
}
}
@@ -33385,24 +31358,24 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
*
* return retval, out_stderr, out_stdout
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3218; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3218; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
__Pyx_XDECREF(__pyx_v_out_stderr);
- __pyx_v_out_stderr = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_v_out_stderr = ((PyObject *)__pyx_t_3);
+ __pyx_t_3 = 0;
}
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L82_try_end;
- __pyx_L75_error:;
+ goto __pyx_L83_try_end;
+ __pyx_L76_error:;
__Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
/* "csamtools.pyx":3212
* with open( stderr_f, "r") as inf:
@@ -33414,10 +31387,10 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
if (__pyx_t_8) {
__Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_2, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_GOTREF(__pyx_t_3);
/* "csamtools.pyx":3213
* out_stderr = inf.readlines()
@@ -33427,24 +31400,24 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* out_stderr = inf.read()
*/
/*with:*/ {
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_21 = PyTuple_New(2); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_21));
__Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_v_stderr_f);
__Pyx_GIVEREF(__pyx_v_stderr_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
+ PyTuple_SET_ITEM(__pyx_t_21, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_21 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_21), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
+ __pyx_t_21 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
__Pyx_GOTREF(__pyx_t_20);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
/*try:*/ {
{
@@ -33453,10 +31426,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
- __Pyx_INCREF(__pyx_t_20);
__Pyx_XDECREF(__pyx_v_inf);
__pyx_v_inf = __pyx_t_20;
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __pyx_t_20 = 0;
/* "csamtools.pyx":3215
* with open( stderr_f, "rb") as inf:
@@ -33498,7 +31470,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_GOTREF(__pyx_t_20);
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_22));
__Pyx_INCREF(__pyx_t_21);
PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_21);
__Pyx_GIVEREF(__pyx_t_21);
@@ -33523,9 +31495,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_ErrRestore(__pyx_t_21, __pyx_t_20, __pyx_t_6);
__pyx_t_21 = 0; __pyx_t_20 = 0; __pyx_t_6 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- goto __pyx_L121;
+ goto __pyx_L120;
}
- __pyx_L121:;
+ __pyx_L120:;
__Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
@@ -33537,7 +31509,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- goto __pyx_L77_except_error;
+ goto __pyx_L78_except_error;
__pyx_L111_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
@@ -33550,18 +31522,18 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
if (__pyx_t_15) {
__pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_184, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
}
}
- goto __pyx_L122;
+ goto __pyx_L121;
__pyx_L104_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L77_except_error;
- __pyx_L122:;
+ goto __pyx_L78_except_error;
+ __pyx_L121:;
}
/* "csamtools.pyx":3216
@@ -33571,38 +31543,38 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* else:
* out_stderr = []
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_20 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__remove); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_20 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__remove); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_INCREF(__pyx_v_stderr_f);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
__Pyx_GIVEREF(__pyx_v_stderr_f);
- __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L77_except_error;}
+ __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
__Pyx_GOTREF(__pyx_t_21);
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L76_exception_handled;
+ goto __pyx_L77_exception_handled;
}
- __pyx_L77_except_error:;
+ __pyx_L78_except_error:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
goto __pyx_L1_error;
- __pyx_L76_exception_handled:;
+ __pyx_L77_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
- __pyx_L82_try_end:;
+ __pyx_L83_try_end:;
}
/* "csamtools.pyx":3220
@@ -33613,23 +31585,21 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
* cdef class SNPCall:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- if (unlikely(!__pyx_v_out_stderr)) { __Pyx_RaiseUnboundLocalError("out_stderr"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- if (unlikely(!__pyx_v_out_stdout)) { __Pyx_RaiseUnboundLocalError("out_stdout"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
+ if (unlikely(!__pyx_v_out_stderr)) { __Pyx_RaiseUnboundLocalError("out_stderr"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }if (unlikely(!__pyx_v_out_stdout)) { __Pyx_RaiseUnboundLocalError("out_stdout"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE_ [...]
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_out_stderr);
- PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_v_out_stderr);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_out_stderr);
__Pyx_GIVEREF(__pyx_v_out_stderr);
__Pyx_INCREF(__pyx_v_out_stdout);
- PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_out_stdout);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_out_stdout);
__Pyx_GIVEREF(__pyx_v_out_stdout);
- __pyx_t_3 = 0;
- __pyx_r = ((PyObject *)__pyx_t_4);
__pyx_t_4 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_2);
+ __pyx_t_2 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -33663,17 +31633,6 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_3tid___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3235
* property tid:
* '''the chromosome ID as is defined in the header'''
@@ -33682,7 +31641,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_se
*
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -33690,7 +31650,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3235);
/* "csamtools.pyx":3236
@@ -33701,7 +31661,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csa
* property pos:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -33720,17 +31680,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_3pos___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3240
* property pos:
* '''nucleotide position of SNP.'''
@@ -33739,7 +31688,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_se
* property reference_base:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -33747,10 +31697,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3240);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -33769,17 +31719,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3244
* property reference_base:
* '''reference base at pos. ``N`` if no reference sequence supplied.'''
@@ -33788,7 +31727,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(PyObject
* property genotype:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -33796,10 +31736,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3244);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&__pyx_v_self->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -33818,17 +31758,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(struct __
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_8genotype___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3248
* property genotype:
* '''the genotype called.'''
@@ -33837,7 +31766,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx
* property consensus_quality:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -33845,10 +31775,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3248);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&__pyx_v_self->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -33867,17 +31797,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3252
* property consensus_quality:
* '''the genotype quality (Phred-scaled).'''
@@ -33886,7 +31805,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObj
* property snp_quality:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -33894,10 +31814,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3252);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -33916,17 +31836,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(struct
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3256
* property snp_quality:
* '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
@@ -33935,7 +31844,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *_
* property mapping_quality:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -33943,10 +31853,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3256);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -33965,17 +31875,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3260
* property mapping_quality:
* '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
@@ -33984,7 +31883,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObjec
* property coverage:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -33992,10 +31892,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct _
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3260);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -34014,17 +31914,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(struct _
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall_8coverage___get__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3264
* property coverage:
* '''coverage or read depth - the number of reads involved in the call.'''
@@ -34033,7 +31922,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx
* def __str__(self):
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -34041,10 +31931,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_RefNannySetupContext("__get__");
__Pyx_TraceCall("__get__", __pyx_f[0], 3264);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -34063,17 +31953,6 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_7SNPCall___str__(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3266
* def __get__(self): return self._coverage
*
@@ -34082,7 +31961,8 @@ static PyObject *__pyx_pw_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self) {
* return "\t".join( map(str, (
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtools_SNPCall *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -34099,7 +31979,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_RefNannySetupContext("__str__");
__Pyx_TraceCall("__str__", __pyx_f[0], 3266);
/* "csamtools.pyx":3268
@@ -34120,7 +32000,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
* self.pos,
* self.reference_base,
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
/* "csamtools.pyx":3270
@@ -34130,7 +32010,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
* self.reference_base,
* self.genotype,
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
/* "csamtools.pyx":3271
@@ -34140,7 +32020,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
* self.genotype,
* self.consensus_quality,
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
/* "csamtools.pyx":3272
@@ -34150,7 +32030,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
* self.consensus_quality,
* self.snp_quality,
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
/* "csamtools.pyx":3273
@@ -34160,7 +32040,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
* self.snp_quality,
* self.mapping_quality,
*/
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
/* "csamtools.pyx":3274
@@ -34170,7 +32050,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
* self.mapping_quality,
* self.coverage ) ) )
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
/* "csamtools.pyx":3275
@@ -34180,7 +32060,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
* self.coverage ) ) )
*
*/
- __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
/* "csamtools.pyx":3276
@@ -34190,10 +32070,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
*
*
*/
- __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_10 = PyTuple_New(8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_10));
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_3);
@@ -34219,7 +32099,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
__pyx_t_8 = 0;
__pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -34230,7 +32110,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
@@ -34264,28 +32144,44 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* Python wrapper */
-static int __pyx_pw_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* "csamtools.pyx":3786
+ * """
+ *
+ * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ *
+ */
+
+static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_reopen;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ char *__pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__");
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3786);
{
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (pos_args) {
+ switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
if (likely(values[0])) kw_args--;
@@ -34297,19 +32193,7 @@ static int __pyx_pw_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self,
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- }
- if (values[1]) {
- } else {
-
- /* "csamtools.pyx":3786
- * """
- *
- * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- *
- */
- __pyx_v_reopen = ((int)1);
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -34335,29 +32219,6 @@ static int __pyx_pw_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self,
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_r = __pyx_pf_9csamtools_12IndexedReads___init__(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
- goto __pyx_L0;
- __pyx_L1_error:;
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
- int __pyx_r;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- char *__pyx_t_3;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__", 0);
- __Pyx_TraceCall("__init__", __pyx_f[0], 3786);
/* "csamtools.pyx":3787
*
@@ -34368,9 +32229,9 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(__pyx_v_self->samfile);
- __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
- __pyx_v_self->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile);
+ __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile = __pyx_v_samfile;
/* "csamtools.pyx":3789
* self.samfile = samfile
@@ -34382,7 +32243,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L3;
+ goto __pyx_L6;
}
/*else*/ {
@@ -34396,7 +32257,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L3:;
+ __pyx_L6:;
/* "csamtools.pyx":3794
* # reopen the file - note that this makes the iterator
@@ -34430,7 +32291,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
* assert self.fp != NULL
*/
__pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
/* "csamtools.pyx":3797
* store = StderrStore()
@@ -34454,7 +32315,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(__pyx_v_self->fp != NULL))) {
+ if (unlikely(!(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
@@ -34467,8 +32328,8 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
* else:
* self.fp = samfile.samfile
*/
- __pyx_v_self->owns_samfile = 1;
- goto __pyx_L4;
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 1;
+ goto __pyx_L7;
}
/*else*/ {
@@ -34479,7 +32340,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
* self.owns_samfile = False
*
*/
- __pyx_v_self->fp = __pyx_v_samfile->samfile;
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
/* "csamtools.pyx":3802
* else:
@@ -34488,9 +32349,9 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
*
* assert samfile.isbam, "can only IndexReads on bam files"
*/
- __pyx_v_self->owns_samfile = 0;
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 0;
}
- __pyx_L4:;
+ __pyx_L7:;
/* "csamtools.pyx":3804
* self.owns_samfile = False
@@ -34521,18 +32382,6 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(struct __pyx_obj_9csamtoo
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_12IndexedReads_2build[] = "IndexedReads.build(self)\nbuild index.";
-static PyObject *__pyx_pw_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("build (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_12IndexedReads_2build(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3806
* assert samfile.isbam, "can only IndexReads on bam files"
*
@@ -34541,7 +32390,9 @@ static PyObject *__pyx_pw_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_sel
*
*/
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self) {
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_9csamtools_12IndexedReads_1build[] = "IndexedReads.build(self)\nbuild index.";
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
int __pyx_v_ret;
bam1_t *__pyx_v_b;
uint64_t __pyx_v_pos;
@@ -34556,7 +32407,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("build", 0);
+ __Pyx_RefNannySetupContext("build");
__Pyx_TraceCall("build", __pyx_f[0], 3806);
/* "csamtools.pyx":3809
@@ -34572,7 +32423,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyList_Type))));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyList_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyList_Type))));
@@ -34581,9 +32432,9 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_GIVEREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_v_self->index);
- __Pyx_DECREF(__pyx_v_self->index);
- __pyx_v_self->index = __pyx_t_3;
+ __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
+ __Pyx_DECREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
+ ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index = __pyx_t_3;
__pyx_t_3 = 0;
/* "csamtools.pyx":3813
@@ -34622,7 +32473,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
* ret = samread( self.fp, b)
* if ret > 0:
*/
- __pyx_v_pos = bam_tell(__pyx_v_self->fp->x.bam);
+ __pyx_v_pos = bam_tell(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp->x.bam);
/* "csamtools.pyx":3820
* while ret > 0:
@@ -34631,7 +32482,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
* if ret > 0:
* qname = _charptr_to_str(bam1_qname( b ))
*/
- __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_b);
+ __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp, __pyx_v_b);
/* "csamtools.pyx":3821
* pos = bam_tell( self.fp.x.bam )
@@ -34663,7 +32514,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
*
* bam_destroy1( b )
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_1 = __Pyx_PyInt_to_py_uint64_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -34672,9 +32523,9 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L5;
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
}
/* "csamtools.pyx":3825
@@ -34702,18 +32553,6 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2build(struct __pyx_obj_9csa
return __pyx_r;
}
-/* Python wrapper */
-static PyObject *__pyx_pw_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static char __pyx_doc_9csamtools_12IndexedReads_4find[] = "IndexedReads.find(self, qname)";
-static PyObject *__pyx_pw_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
- PyObject *__pyx_r = 0;
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("find (wrapper)", 0);
- __pyx_r = __pyx_pf_9csamtools_12IndexedReads_4find(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
/* "csamtools.pyx":3827
* bam_destroy1( b )
*
@@ -34722,7 +32561,9 @@ static PyObject *__pyx_pw_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
*/
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname) {
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static char __pyx_doc_9csamtools_12IndexedReads_2find[] = "IndexedReads.find(self, qname)";
+static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -34733,7 +32574,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("find", 0);
+ __Pyx_RefNannySetupContext("find");
__Pyx_TraceCall("find", __pyx_f[0], 3827);
/* "csamtools.pyx":3828
@@ -34743,7 +32584,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
* else:
*/
- __pyx_t_1 = ((PySequence_Contains(__pyx_v_self->index, __pyx_v_qname))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PySequence_Contains(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
/* "csamtools.pyx":3829
@@ -34754,13 +32595,13 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam
* raise KeyError( "read %s not found" % qname )
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self->samfile));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
+ __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
@@ -34770,14 +32611,14 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam
__Pyx_GOTREF(__pyx_t_4);
if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L3;
+ goto __pyx_L5;
}
/*else*/ {
@@ -34791,7 +32632,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam
__pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_186), __pyx_v_qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
@@ -34802,7 +32643,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L3:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -34819,15 +32660,6 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_4find(struct __pyx_obj_9csam
return __pyx_r;
}
-/* Python wrapper */
-static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self) {
- __Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self));
- __Pyx_RefNannyFinishContext();
-}
-
/* "csamtools.pyx":3833
* raise KeyError( "read %s not found" % qname )
*
@@ -34836,10 +32668,11 @@ static void __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_se
*
*/
-static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9csamtools_IndexedReads *__pyx_v_self) {
+static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_RefNannySetupContext("__dealloc__");
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 3833);
/* "csamtools.pyx":3834
@@ -34849,11 +32682,11 @@ static void __pyx_pf_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_9cs
*
* __all__ = ["Samfile",
*/
- if (__pyx_v_self->owns_samfile) {
- samclose(__pyx_v_self->fp);
- goto __pyx_L3;
+ if (((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile) {
+ samclose(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp);
+ goto __pyx_L5;
}
- __pyx_L3:;
+ __pyx_L5:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
@@ -34866,7 +32699,7 @@ static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a,
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_Fastafile *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile;
- if (__pyx_pw_9csamtools_9Fastafile_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
@@ -34877,7 +32710,7 @@ static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_9Fastafile_11__dealloc__(o);
+ __pyx_pf_9csamtools_9Fastafile_5__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -34886,14 +32719,14 @@ static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
}
static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_9Fastafile_8filename_1__get__(o);
+ return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_2_isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_7_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6_open)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_9close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_8close)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_9csamtools_9Fastafile_13fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_12fetch)},
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_1_isOpen)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_4close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_4close)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_6fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6fetch)},
{0, 0, 0, 0}
};
@@ -34961,7 +32794,7 @@ static PyNumberMethods __pyx_tp_as_number_Fastafile = {
};
static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
- __pyx_pw_9csamtools_9Fastafile_5__len__, /*sq_length*/
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
@@ -34974,7 +32807,7 @@ static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
};
static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pw_9csamtools_9Fastafile_5__len__, /*mp_length*/
+ __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
@@ -35067,7 +32900,7 @@ static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_11AlignedRead_3__dealloc__(o);
+ __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -35076,12 +32909,12 @@ static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5qname_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5qname___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5qname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35090,12 +32923,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5cigar_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5cigar_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35104,12 +32937,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35118,12 +32951,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObj
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3seq_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3seq___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3seq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35132,12 +32965,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4qual_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4qual___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4qual_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35146,32 +32979,32 @@ static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5query_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5query___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5qqual_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_6qstart_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4qend_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4qend___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4qlen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4tags_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4tags___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4tags_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35180,12 +33013,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4flag_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4flag_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35194,12 +33027,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5rname_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5rname_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35208,12 +33041,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3tid_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3tid_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35222,12 +33055,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3pos_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3pos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35236,12 +33069,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_3bin_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_3bin_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35250,24 +33083,24 @@ static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4rlen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4aend_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4alen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4mapq_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4mapq_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35276,12 +33109,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4mrnm_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4mrnm_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35290,12 +33123,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5rnext_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5rnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35304,12 +33137,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4mpos_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4mpos_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35318,12 +33151,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5pnext_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5pnext_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35332,12 +33165,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_5isize_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_5isize_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35346,12 +33179,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_4tlen_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_4tlen_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35360,12 +33193,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_paired_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_paired_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35374,12 +33207,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObjec
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35388,12 +33221,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, Py
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35402,12 +33235,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObj
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35416,12 +33249,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o,
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35430,12 +33263,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObje
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35444,12 +33277,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, P
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read1_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read1_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35458,12 +33291,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read2_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_8is_read2_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35472,12 +33305,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35486,12 +33319,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyOb
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35500,12 +33333,12 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObjec
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o);
}
static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v);
+ return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -35514,18 +33347,18 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyOb
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_9positions_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o);
+ return __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = {
- {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_7compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6compare)},
- {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_11overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_10overlap)},
- {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_13opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_12opt)},
- {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pw_9csamtools_11AlignedRead_15fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_14fancy_str)},
+ {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_3compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_3compare)},
+ {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_5overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_5overlap)},
+ {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_6opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6opt)},
+ {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_7fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_7fancy_str)},
{0, 0, 0, 0}
};
@@ -35688,9 +33521,9 @@ static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
&__pyx_tp_as_number_AlignedRead, /*tp_as_number*/
&__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/
&__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
- __pyx_pw_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/
+ __pyx_pf_9csamtools_11AlignedRead_4__hash__, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_11AlignedRead_5__str__, /*tp_str*/
+ __pyx_pf_9csamtools_11AlignedRead_2__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
@@ -35710,7 +33543,7 @@ static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_11AlignedRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
@@ -35733,7 +33566,7 @@ static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, P
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_Samfile *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
- if (__pyx_pw_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
@@ -35744,7 +33577,7 @@ static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_7Samfile_31__dealloc__(o);
+ __pyx_pf_9csamtools_7Samfile_15__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -35753,57 +33586,57 @@ static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_8filename_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_11nreferences_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_10references_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_7lengths_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_6mapped_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_8unmapped_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_4text_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7Samfile_6header_1__get__(o);
+ return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4_hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_open)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8gettid)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10getrname)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12_parseRegion)},
- {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14reset)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_17seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_19tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_21fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_20fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_23mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_22mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_25count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_24count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_27pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_26pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_29close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_28close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_32write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_34__enter__)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_36__exit__)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_38_buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_42__next__)},
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)},
+ {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)},
+ {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)},
+ {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)},
+ {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)},
+ {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)},
+ {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)},
+ {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)},
+ {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)},
+ {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)},
+ {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)},
+ {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)},
+ {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)},
+ {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)},
{0, 0, 0, 0}
};
@@ -35947,8 +33780,8 @@ static PyTypeObject __pyx_type_9csamtools_Samfile = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_7Samfile_41__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_7Samfile_43__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/
__pyx_methods_9csamtools_Samfile, /*tp_methods*/
0, /*tp_members*/
__pyx_getsets_9csamtools_Samfile, /*tp_getset*/
@@ -35984,16 +33817,16 @@ static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_3tid_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_1n_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o);
}
static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
if (v) {
- return __pyx_pw_9csamtools_11PileupProxy_1n_3__set__(o, v);
+ return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -36002,11 +33835,11 @@ static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, vo
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_3pos_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_11PileupProxy_7pileups_1__get__(o);
+ return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
@@ -36139,7 +33972,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
&__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_11PileupProxy_3__str__, /*tp_str*/
+ __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/
@@ -36159,7 +33992,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_11PileupProxy_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
@@ -36209,31 +34042,31 @@ static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) {
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_9alignment_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_4qpos_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_5indel_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_6is_del_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_7is_head_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_7is_tail_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_10PileupRead_5level_1__get__(o);
+ return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
@@ -36369,7 +34202,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupRead = {
&__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_10PileupRead_3__str__, /*tp_str*/
+ __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
@@ -36389,7 +34222,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupRead = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_10PileupRead_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
@@ -36581,7 +34414,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyOb
p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion;
p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
@@ -36593,7 +34426,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_17IteratorRowRegion_7__dealloc__(o);
+ __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -36627,7 +34460,7 @@ static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
}
static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_4__next__)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)},
{0, 0, 0, 0}
};
@@ -36759,8 +34592,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
__pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
@@ -36792,7 +34625,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObjec
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
- if (__pyx_pw_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
@@ -36803,7 +34636,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_14IteratorRowAll_7__dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -36812,7 +34645,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
}
static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_4__next__)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)},
{0, 0, 0, 0}
};
@@ -36944,8 +34777,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
@@ -36977,7 +34810,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyO
p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
@@ -37021,8 +34854,8 @@ static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
}
static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pw_9csamtools_18IteratorRowAllRefs_3nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_2nextiter)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__)},
+ {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)},
{0, 0, 0, 0}
};
@@ -37154,8 +34987,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
__pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
@@ -37188,7 +35021,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, P
p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
p->positions = Py_None; Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_20IteratorRowSelection_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
@@ -37200,7 +35033,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_20IteratorRowSelection_7__dealloc__(o);
+ __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -37234,7 +35067,7 @@ static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
}
static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_4__next__)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)},
{0, 0, 0, 0}
};
@@ -37366,8 +35199,8 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
__pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/
- __pyx_pw_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
@@ -37403,7 +35236,7 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObjec
p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
p->stepper = Py_None; Py_INCREF(Py_None);
- if (__pyx_pw_9csamtools_14IteratorColumn_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
@@ -37415,7 +35248,7 @@ static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_14IteratorColumn_9__dealloc__(o);
+ __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -37464,12 +35297,12 @@ static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
}
static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_14IteratorColumn_7seq_len_1__get__(o);
+ return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_4addReference)},
- {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pw_9csamtools_14IteratorColumn_7hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_6hasReference)},
+ {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)},
+ {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)},
{0, 0, 0, 0}
};
@@ -37606,7 +35439,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
__pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/
0, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
0, /*tp_members*/
@@ -37639,14 +35472,14 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, P
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
- if (__pyx_pw_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_2__next__)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)},
{0, 0, 0, 0}
};
@@ -37779,7 +35612,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pw_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
@@ -37811,14 +35644,14 @@ static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t,
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
- if (__pyx_pw_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)},
{0, 0, 0, 0}
};
@@ -37951,7 +35784,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
- __pyx_pw_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/
+ __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/
__pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
@@ -37992,7 +35825,7 @@ static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) {
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_9csamtools_12IndexedReads_7__dealloc__(o);
+ __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -38027,8 +35860,8 @@ static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) {
}
static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = {
- {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pw_9csamtools_12IndexedReads_3build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2build)},
- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_4find)},
+ {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_1build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_1build)},
+ {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)},
{0, 0, 0, 0}
};
@@ -38170,7 +36003,7 @@ static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_9csamtools_12IndexedReads_1__init__, /*tp_init*/
+ __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_9csamtools_IndexedReads, /*tp_new*/
0, /*tp_free*/
@@ -38197,35 +36030,35 @@ static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_3tid_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_3pos_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_14reference_base_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_8genotype_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_17consensus_quality_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_11snp_quality_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_15mapping_quality_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o);
}
static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
- return __pyx_pw_9csamtools_7SNPCall_8coverage_1__get__(o);
+ return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
}
static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
@@ -38362,7 +36195,7 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = {
&__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_9csamtools_7SNPCall_1__str__, /*tp_str*/
+ __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
@@ -38398,9 +36231,219 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = {
#endif
};
+static PyObject *__pyx_tp_new_9csamtools___pyx_Generator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_Generator_object *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
+ if (!o) return 0;
+ p = ((struct __pyx_Generator_object *)o);
+ p->exc_type = 0;
+ p->exc_value = 0;
+ p->exc_traceback = 0;
+ return o;
+}
+
+static void __pyx_tp_dealloc_9csamtools___pyx_Generator(PyObject *o) {
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ Py_XDECREF(p->exc_type);
+ Py_XDECREF(p->exc_value);
+ Py_XDECREF(p->exc_traceback);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_9csamtools___pyx_Generator(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ if (p->exc_type) {
+ e = (*v)(p->exc_type, a); if (e) return e;
+ }
+ if (p->exc_value) {
+ e = (*v)(p->exc_value, a); if (e) return e;
+ }
+ if (p->exc_traceback) {
+ e = (*v)(p->exc_traceback, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_9csamtools___pyx_Generator(PyObject *o) {
+ struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->exc_type);
+ p->exc_type = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->exc_value);
+ p->exc_value = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->exc_traceback);
+ p->exc_traceback = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_9csamtools___pyx_Generator[] = {
+ {__Pyx_NAMESTR("send"), (PyCFunction)__Pyx_Generator_Send, METH_O, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__Pyx_Generator_Close, METH_NOARGS, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("throw"), (PyCFunction)__Pyx_Generator_Throw, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number___pyx_Generator = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence___pyx_Generator = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping___pyx_Generator = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer___pyx_Generator = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_Generator_type = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("csamtools.__pyx_Generator"), /*tp_name*/
+ sizeof(struct __pyx_Generator_object), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_9csamtools___pyx_Generator, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number___pyx_Generator, /*tp_as_number*/
+ &__pyx_tp_as_sequence___pyx_Generator, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping___pyx_Generator, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer___pyx_Generator, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_9csamtools___pyx_Generator, /*tp_traverse*/
+ __pyx_tp_clear_9csamtools___pyx_Generator, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ PyObject_SelfIter, /*tp_iter*/
+ __Pyx_Generator_Next, /*tp_iternext*/
+ __pyx_methods_9csamtools___pyx_Generator, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_9csamtools___pyx_Generator, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct__genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+ PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k);
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o);
p->__pyx_v_x = 0;
@@ -38416,12 +36459,13 @@ static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr(PyObject *o)
Py_XDECREF(p->__pyx_v_y);
Py_XDECREF(p->__pyx_t_0);
Py_XDECREF(p->__pyx_t_1);
- (*Py_TYPE(o)->tp_free)(o);
+ __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
}
static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
+ e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e;
if (p->__pyx_v_x) {
e = (*v)(p->__pyx_v_x, a); if (e) return e;
}
@@ -38440,6 +36484,7 @@ static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o,
static int __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
PyObject* tmp;
+ __pyx_tp_clear_9csamtools___pyx_Generator(o);
tmp = ((PyObject*)p->__pyx_v_x);
p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -38615,7 +36660,7 @@ static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+ PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k);
if (!o) return 0;
p = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o);
p->__pyx_v_x = 0;
@@ -38631,12 +36676,13 @@ static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o
Py_XDECREF(p->__pyx_v_y);
Py_XDECREF(p->__pyx_t_0);
Py_XDECREF(p->__pyx_t_1);
- (*Py_TYPE(o)->tp_free)(o);
+ __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
}
static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e;
if (p->__pyx_v_x) {
e = (*v)(p->__pyx_v_x, a); if (e) return e;
}
@@ -38655,6 +36701,7 @@ static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o
static int __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
PyObject* tmp;
+ __pyx_tp_clear_9csamtools___pyx_Generator(o);
tmp = ((PyObject*)p->__pyx_v_x);
p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -38913,12 +36960,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
{&__pyx_n_s_249, __pyx_k_249, sizeof(__pyx_k_249), 0, 0, 1, 1},
{&__pyx_kp_s_251, __pyx_k_251, sizeof(__pyx_k_251), 0, 0, 1, 0},
+ {&__pyx_kp_s_254, __pyx_k_254, sizeof(__pyx_k_254), 0, 0, 1, 0},
+ {&__pyx_kp_s_255, __pyx_k_255, sizeof(__pyx_k_255), 0, 0, 1, 0},
{&__pyx_kp_s_256, __pyx_k_256, sizeof(__pyx_k_256), 0, 0, 1, 0},
- {&__pyx_kp_s_257, __pyx_k_257, sizeof(__pyx_k_257), 0, 0, 1, 0},
- {&__pyx_kp_s_266, __pyx_k_266, sizeof(__pyx_k_266), 0, 0, 1, 0},
- {&__pyx_kp_s_273, __pyx_k_273, sizeof(__pyx_k_273), 0, 0, 1, 0},
+ {&__pyx_kp_s_262, __pyx_k_262, sizeof(__pyx_k_262), 0, 0, 1, 0},
{&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
- {&__pyx_kp_s_290, __pyx_k_290, sizeof(__pyx_k_290), 0, 0, 1, 0},
{&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
{&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
{&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
@@ -39004,6 +37050,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__PI, __pyx_k__PI, sizeof(__pyx_k__PI), 0, 0, 1, 1},
{&__pyx_n_s__PL, __pyx_k__PL, sizeof(__pyx_k__PL), 0, 0, 1, 1},
{&__pyx_n_s__PN, __pyx_k__PN, sizeof(__pyx_k__PN), 0, 0, 1, 1},
+ {&__pyx_n_s__PP, __pyx_k__PP, sizeof(__pyx_k__PP), 0, 0, 1, 1},
{&__pyx_n_s__PU, __pyx_k__PU, sizeof(__pyx_k__PU), 0, 0, 1, 1},
{&__pyx_n_s__PileupColumn, __pyx_k__PileupColumn, sizeof(__pyx_k__PileupColumn), 0, 0, 1, 1},
{&__pyx_n_s__PileupProxy, __pyx_k__PileupProxy, sizeof(__pyx_k__PileupProxy), 0, 0, 1, 1},
@@ -39046,7 +37093,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s___open, __pyx_k___open, sizeof(__pyx_k___open), 0, 0, 1, 1},
{&__pyx_n_s___parseRegion, __pyx_k___parseRegion, sizeof(__pyx_k___parseRegion), 0, 0, 1, 1},
{&__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},
@@ -39059,7 +37105,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__c, __pyx_k__c, sizeof(__pyx_k__c), 0, 0, 1, 1},
{&__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},
@@ -39103,7 +37148,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__id, __pyx_k__id, sizeof(__pyx_k__id), 0, 0, 1, 1},
{&__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},
@@ -39137,13 +37181,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__nextiter, __pyx_k__nextiter, sizeof(__pyx_k__nextiter), 0, 0, 1, 1},
{&__pyx_n_s__nreferences, __pyx_k__nreferences, sizeof(__pyx_k__nreferences), 0, 0, 1, 1},
{&__pyx_n_s__object, __pyx_k__object, sizeof(__pyx_k__object), 0, 0, 1, 1},
- {&__pyx_n_s__ofd, __pyx_k__ofd, sizeof(__pyx_k__ofd), 0, 0, 1, 1},
{&__pyx_n_s__offset, __pyx_k__offset, sizeof(__pyx_k__offset), 0, 0, 1, 1},
{&__pyx_n_s__open, __pyx_k__open, sizeof(__pyx_k__open), 0, 0, 1, 1},
{&__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},
- {&__pyx_n_s__out_stderr, __pyx_k__out_stderr, sizeof(__pyx_k__out_stderr), 0, 0, 1, 1},
- {&__pyx_n_s__out_stdout, __pyx_k__out_stdout, sizeof(__pyx_k__out_stdout), 0, 0, 1, 1},
{&__pyx_n_s__pack_into, __pyx_k__pack_into, sizeof(__pyx_k__pack_into), 0, 0, 1, 1},
{&__pyx_n_s__path, __pyx_k__path, sizeof(__pyx_k__path), 0, 0, 1, 1},
{&__pyx_n_s__pileups, __pyx_k__pileups, sizeof(__pyx_k__pileups), 0, 0, 1, 1},
@@ -39176,7 +37217,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__remove, __pyx_k__remove, sizeof(__pyx_k__remove), 0, 0, 1, 1},
{&__pyx_n_s__reopen, __pyx_k__reopen, sizeof(__pyx_k__reopen), 0, 0, 1, 1},
{&__pyx_n_s__restore, __pyx_k__restore, sizeof(__pyx_k__restore), 0, 0, 1, 1},
- {&__pyx_n_s__retval, __pyx_k__retval, sizeof(__pyx_k__retval), 0, 0, 1, 1},
{&__pyx_n_s__rlen, __pyx_k__rlen, sizeof(__pyx_k__rlen), 0, 0, 1, 1},
{&__pyx_n_s__rname, __pyx_k__rname, sizeof(__pyx_k__rname), 0, 0, 1, 1},
{&__pyx_n_s__s, __pyx_k__s, sizeof(__pyx_k__s), 0, 0, 1, 1},
@@ -39194,12 +37234,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1},
{&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1},
{&__pyx_n_s__stderr, __pyx_k__stderr, sizeof(__pyx_k__stderr), 0, 0, 1, 1},
- {&__pyx_n_s__stderr_f, __pyx_k__stderr_f, sizeof(__pyx_k__stderr_f), 0, 0, 1, 1},
- {&__pyx_n_s__stderr_h, __pyx_k__stderr_h, sizeof(__pyx_k__stderr_h), 0, 0, 1, 1},
{&__pyx_n_s__stdout, __pyx_k__stdout, sizeof(__pyx_k__stdout), 0, 0, 1, 1},
- {&__pyx_n_s__stdout_f, __pyx_k__stdout_f, sizeof(__pyx_k__stdout_f), 0, 0, 1, 1},
- {&__pyx_n_s__stdout_h, __pyx_k__stdout_h, sizeof(__pyx_k__stdout_h), 0, 0, 1, 1},
- {&__pyx_n_s__stdout_save, __pyx_k__stdout_save, sizeof(__pyx_k__stdout_save), 0, 0, 1, 1},
{&__pyx_n_s__stepper, __pyx_k__stepper, sizeof(__pyx_k__stepper), 0, 0, 1, 1},
{&__pyx_n_s__streams, __pyx_k__streams, sizeof(__pyx_k__streams), 0, 0, 1, 1},
{&__pyx_n_s__strip, __pyx_k__strip, sizeof(__pyx_k__strip), 0, 0, 1, 1},
@@ -39256,7 +37291,7 @@ static int __Pyx_InitCachedBuiltins(void) {
static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
+ __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants");
/* "csamtools.pyx":64
* return s
@@ -39266,7 +37301,7 @@ static int __Pyx_InitCachedConstants(void) {
* raise TypeError, u"Argument must be string, bytes or unicode."
*/
__pyx_k_tuple_2 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_2));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_2, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -39280,7 +37315,7 @@ static int __Pyx_InitCachedConstants(void) {
* # assume unicode
*/
__pyx_k_tuple_4 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_4);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_4));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_4, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -39294,7 +37329,7 @@ static int __Pyx_InitCachedConstants(void) {
* return faidx_fetch_nseq(self.fastafile)
*/
__pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_8);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_8));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
@@ -39308,7 +37343,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_11 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_11);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_11));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_11, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39322,7 +37357,7 @@ static int __Pyx_InitCachedConstants(void) {
* cdef int length
*/
__pyx_k_tuple_12 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_12);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_12));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_12, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39336,7 +37371,7 @@ static int __Pyx_InitCachedConstants(void) {
* if end is None: end = max_pos -1
*/
__pyx_k_tuple_14 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_14);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_14));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_13));
PyTuple_SET_ITEM(__pyx_k_tuple_14, 0, ((PyObject *)__pyx_kp_s_13));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_13));
@@ -39350,7 +37385,7 @@ static int __Pyx_InitCachedConstants(void) {
* region,
*/
__pyx_k_tuple_20 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_20);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_20));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_20, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -39364,7 +37399,7 @@ static int __Pyx_InitCachedConstants(void) {
* #cfilename = filename.encode(_FILENAME_ENCODING)
*/
__pyx_k_tuple_25 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_25);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_25));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_25, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -39378,7 +37413,7 @@ static int __Pyx_InitCachedConstants(void) {
* return pysam_reference2tid( self.samfile.header, reference )
*/
__pyx_k_tuple_39 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_39);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_39));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_39, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39392,7 +37427,7 @@ static int __Pyx_InitCachedConstants(void) {
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
__pyx_k_tuple_40 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_40);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_40));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_40, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39406,7 +37441,7 @@ static int __Pyx_InitCachedConstants(void) {
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
__pyx_k_tuple_42 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_42);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_42));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_42, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39420,7 +37455,7 @@ static int __Pyx_InitCachedConstants(void) {
* rtid = self.gettid( reference )
*/
__pyx_k_tuple_44 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_44);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_44));
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
@@ -39443,7 +37478,7 @@ static int __Pyx_InitCachedConstants(void) {
* raise NotImplementedError("seek only available in bam files")
*/
__pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_47);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_47));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39457,7 +37492,7 @@ static int __Pyx_InitCachedConstants(void) {
* raise OSError("seek no available in streams")
*/
__pyx_k_tuple_49 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_49);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_49));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
PyTuple_SET_ITEM(__pyx_k_tuple_49, 0, ((PyObject *)__pyx_kp_s_48));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
@@ -39471,7 +37506,7 @@ static int __Pyx_InitCachedConstants(void) {
* return bam_seek( self.samfile.x.bam, offset, where )
*/
__pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_51);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_51));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_50));
PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, ((PyObject *)__pyx_kp_s_50));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_50));
@@ -39485,7 +37520,7 @@ static int __Pyx_InitCachedConstants(void) {
* raise NotImplementedError("seek only available in bam files")
*/
__pyx_k_tuple_52 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_52);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_52));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39499,7 +37534,7 @@ static int __Pyx_InitCachedConstants(void) {
* return bam_tell( self.samfile.x.bam )
*/
__pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_53);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_53));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
PyTuple_SET_ITEM(__pyx_k_tuple_53, 0, ((PyObject *)__pyx_kp_s_48));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
@@ -39513,7 +37548,7 @@ static int __Pyx_InitCachedConstants(void) {
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
__pyx_k_tuple_55 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_55);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_55));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39527,7 +37562,7 @@ static int __Pyx_InitCachedConstants(void) {
* if callback:
*/
__pyx_k_tuple_57 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_57);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_57));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
PyTuple_SET_ITEM(__pyx_k_tuple_57, 0, ((PyObject *)__pyx_kp_s_56));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
@@ -39541,7 +37576,7 @@ static int __Pyx_InitCachedConstants(void) {
* return bam_fetch(self.samfile.x.bam,
*/
__pyx_k_tuple_59 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_59);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_59));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
PyTuple_SET_ITEM(__pyx_k_tuple_59, 0, ((PyObject *)__pyx_kp_s_58));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
@@ -39555,7 +37590,7 @@ static int __Pyx_InitCachedConstants(void) {
* self.index,
*/
__pyx_k_tuple_61 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_61);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_61));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
PyTuple_SET_ITEM(__pyx_k_tuple_61, 0, ((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
@@ -39569,7 +37604,7 @@ static int __Pyx_InitCachedConstants(void) {
* if callback:
*/
__pyx_k_tuple_63 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_63);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_63));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_62));
PyTuple_SET_ITEM(__pyx_k_tuple_63, 0, ((PyObject *)__pyx_kp_s_62));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_62));
@@ -39583,7 +37618,7 @@ static int __Pyx_InitCachedConstants(void) {
* if self.samfile.header == NULL:
*/
__pyx_k_tuple_65 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_65);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_65));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_64));
PyTuple_SET_ITEM(__pyx_k_tuple_65, 0, ((PyObject *)__pyx_kp_s_64));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_64));
@@ -39597,7 +37632,7 @@ static int __Pyx_InitCachedConstants(void) {
* # check if targets are defined
*/
__pyx_k_tuple_67 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_67);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_67));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
PyTuple_SET_ITEM(__pyx_k_tuple_67, 0, ((PyObject *)__pyx_kp_s_66));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
@@ -39611,7 +37646,7 @@ static int __Pyx_InitCachedConstants(void) {
* return IteratorRowAll( self, reopen=reopen )
*/
__pyx_k_tuple_68 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_68);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_68));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
PyTuple_SET_ITEM(__pyx_k_tuple_68, 0, ((PyObject *)__pyx_kp_s_66));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
@@ -39625,7 +37660,7 @@ static int __Pyx_InitCachedConstants(void) {
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
__pyx_k_tuple_72 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_72);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_72));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_71));
PyTuple_SET_ITEM(__pyx_k_tuple_72, 0, ((PyObject *)__pyx_kp_s_71));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_71));
@@ -39639,7 +37674,7 @@ static int __Pyx_InitCachedConstants(void) {
* region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
__pyx_k_tuple_74 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_74);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_74));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_74, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39653,7 +37688,7 @@ static int __Pyx_InitCachedConstants(void) {
* if not region:
*/
__pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_75);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_75));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_kp_s_56));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
@@ -39667,7 +37702,7 @@ static int __Pyx_InitCachedConstants(void) {
* bam_fetch(self.samfile.x.bam,
*/
__pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_77);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_77));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
@@ -39681,7 +37716,7 @@ static int __Pyx_InitCachedConstants(void) {
* self.index,
*/
__pyx_k_tuple_78 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_78);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_78));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
@@ -39695,7 +37730,7 @@ static int __Pyx_InitCachedConstants(void) {
* def pileup( self,
*/
__pyx_k_tuple_80 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_80);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_80));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_79));
PyTuple_SET_ITEM(__pyx_k_tuple_80, 0, ((PyObject *)__pyx_kp_s_79));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_79));
@@ -39709,7 +37744,7 @@ static int __Pyx_InitCachedConstants(void) {
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
__pyx_k_tuple_81 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_81);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_81));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_81, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39723,7 +37758,7 @@ static int __Pyx_InitCachedConstants(void) {
* if callback:
*/
__pyx_k_tuple_83 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_83);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_83));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_82));
PyTuple_SET_ITEM(__pyx_k_tuple_83, 0, ((PyObject *)__pyx_kp_s_82));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_82));
@@ -39737,7 +37772,7 @@ static int __Pyx_InitCachedConstants(void) {
* buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback )
*/
__pyx_k_tuple_84 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_84);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_84));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
PyTuple_SET_ITEM(__pyx_k_tuple_84, 0, ((PyObject *)__pyx_kp_s_58));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
@@ -39751,7 +37786,7 @@ static int __Pyx_InitCachedConstants(void) {
* def close( self ):
*/
__pyx_k_tuple_86 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_86);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_86));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_85));
PyTuple_SET_ITEM(__pyx_k_tuple_86, 0, ((PyObject *)__pyx_kp_s_85));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
@@ -39765,7 +37800,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_87 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_87);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_87));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_87, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39779,7 +37814,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_88 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_88);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_88));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_88, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39793,7 +37828,7 @@ static int __Pyx_InitCachedConstants(void) {
* for x from 0 <= x < self.samfile.header.n_targets:
*/
__pyx_k_tuple_89 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_89);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_89));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_89, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39807,7 +37842,7 @@ static int __Pyx_InitCachedConstants(void) {
* for x from 0 <= x < self.samfile.header.n_targets:
*/
__pyx_k_tuple_90 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_90)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_90);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_90));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_90, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39821,7 +37856,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_91 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_91)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_91);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_91));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_91, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39835,7 +37870,7 @@ static int __Pyx_InitCachedConstants(void) {
* cdef int tid
*/
__pyx_k_tuple_93 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_93)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_93);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_93));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_92));
PyTuple_SET_ITEM(__pyx_k_tuple_93, 0, ((PyObject *)__pyx_kp_s_92));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_92));
@@ -39849,7 +37884,7 @@ static int __Pyx_InitCachedConstants(void) {
* cdef int tid
*/
__pyx_k_tuple_94 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_94)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_94);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_94));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_94, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39863,7 +37898,7 @@ static int __Pyx_InitCachedConstants(void) {
* cdef uint32_t total = 0
*/
__pyx_k_tuple_96 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_96)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_96);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_96));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_95));
PyTuple_SET_ITEM(__pyx_k_tuple_96, 0, ((PyObject *)__pyx_kp_s_95));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_95));
@@ -39877,7 +37912,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_97 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_97);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_97));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_97, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39891,7 +37926,7 @@ static int __Pyx_InitCachedConstants(void) {
* result = {}
*/
__pyx_k_tuple_98 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_98);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_98));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_98, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -39905,7 +37940,7 @@ static int __Pyx_InitCachedConstants(void) {
* assert line.startswith("@"), "header line without '@': '%s'" % line
*/
__pyx_k_tuple_99 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_99)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_99);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_99));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
PyTuple_SET_ITEM(__pyx_k_tuple_99, 0, ((PyObject *)__pyx_kp_s_6));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
@@ -39919,7 +37954,7 @@ static int __Pyx_InitCachedConstants(void) {
* record = fields[0]
*/
__pyx_k_tuple_101 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_101)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_101);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_101));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_100));
PyTuple_SET_ITEM(__pyx_k_tuple_101, 0, ((PyObject *)__pyx_kp_s_100));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_100));
@@ -39933,7 +37968,7 @@ static int __Pyx_InitCachedConstants(void) {
* assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
*/
__pyx_k_tuple_103 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_103);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_103));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
PyTuple_SET_ITEM(__pyx_k_tuple_103, 0, ((PyObject *)__pyx_kp_s_5));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
@@ -39947,7 +37982,7 @@ static int __Pyx_InitCachedConstants(void) {
* # lowercase are permitted for user fields
*/
__pyx_k_tuple_106 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_106)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_106);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_106));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_105));
PyTuple_SET_ITEM(__pyx_k_tuple_106, 0, ((PyObject *)__pyx_kp_s_105));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_105));
@@ -39964,7 +37999,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_112 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_112)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_112);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_112));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_112, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -39978,7 +38013,7 @@ static int __Pyx_InitCachedConstants(void) {
* dest.target_len[x] = seqlen
*/
__pyx_k_tuple_114 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_114)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_114);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_114));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_114, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -39992,7 +38027,7 @@ static int __Pyx_InitCachedConstants(void) {
* raise NotImplementedError( "can not iterate over samfile without header")
*/
__pyx_k_tuple_115 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_115)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_115);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_115));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_115, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -40006,7 +38041,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_117 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_117)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_117);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_117));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_116));
PyTuple_SET_ITEM(__pyx_k_tuple_117, 0, ((PyObject *)__pyx_kp_s_116));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_116));
@@ -40020,7 +38055,7 @@ static int __Pyx_InitCachedConstants(void) {
* if not samfile._hasIndex():
*/
__pyx_k_tuple_118 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_118)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_118);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_118));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_118, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -40034,7 +38069,7 @@ static int __Pyx_InitCachedConstants(void) {
* # makes sure that samfile stays alive as long as the
*/
__pyx_k_tuple_120 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_120)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_120);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_120));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_119));
PyTuple_SET_ITEM(__pyx_k_tuple_120, 0, ((PyObject *)__pyx_kp_s_119));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_119));
@@ -40048,7 +38083,7 @@ static int __Pyx_InitCachedConstants(void) {
* if samfile.isbam: mode = b"rb"
*/
__pyx_k_tuple_121 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_121)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_121);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_121));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_121, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -40062,7 +38097,7 @@ static int __Pyx_InitCachedConstants(void) {
* self.tid = -1
*/
__pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_122);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_122));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
PyTuple_SET_ITEM(__pyx_k_tuple_122, 0, ((PyObject *)__pyx_kp_s_60));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
@@ -40076,7 +38111,7 @@ static int __Pyx_InitCachedConstants(void) {
* if not samfile._isOpen():
*/
__pyx_k_tuple_123 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_123)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_123);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_123));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_123, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -40090,7 +38125,7 @@ static int __Pyx_InitCachedConstants(void) {
* assert samfile.isbam, "can only use this iterator on bam files"
*/
__pyx_k_tuple_124 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_124);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_124));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
PyTuple_SET_ITEM(__pyx_k_tuple_124, 0, ((PyObject *)__pyx_kp_s_10));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
@@ -40104,7 +38139,7 @@ static int __Pyx_InitCachedConstants(void) {
* if self.plp == NULL:
*/
__pyx_k_tuple_130 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_130)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_130);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_130));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
PyTuple_SET_ITEM(__pyx_k_tuple_130, 0, ((PyObject *)__pyx_kp_s_129));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
@@ -40118,7 +38153,7 @@ static int __Pyx_InitCachedConstants(void) {
* # return result, if within same reference
*/
__pyx_k_tuple_131 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_131);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_131));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
PyTuple_SET_ITEM(__pyx_k_tuple_131, 0, ((PyObject *)__pyx_kp_s_129));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
@@ -40132,7 +38167,7 @@ static int __Pyx_InitCachedConstants(void) {
* return "\t".join(map(str, (self.qname,
*/
__pyx_k_tuple_133 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_133);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_133));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_133, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -40146,7 +38181,7 @@ static int __Pyx_InitCachedConstants(void) {
* self.flag,
*/
__pyx_k_tuple_134 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_134)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_134);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_134));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_134, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -40160,7 +38195,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_139 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_139)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_139);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_139));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_139, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -40174,7 +38209,7 @@ static int __Pyx_InitCachedConstants(void) {
* len(value)] + list(value) )
*/
__pyx_k_tuple_142 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_142)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_142);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_142));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_142, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -40188,7 +38223,7 @@ static int __Pyx_InitCachedConstants(void) {
* fmts.append( datafmt )
*/
__pyx_k_tuple_143 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_143)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_143);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_143));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_143, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -40202,7 +38237,7 @@ static int __Pyx_InitCachedConstants(void) {
* fmt, pytype = "2scc", 'A'
*/
__pyx_k_tuple_144 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_144)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_144);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_144));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_144, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -40216,7 +38251,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_146 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_146)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_146);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_146));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
PyTuple_SET_ITEM(__pyx_k_tuple_146, 0, ((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
@@ -40230,7 +38265,7 @@ static int __Pyx_InitCachedConstants(void) {
* def __str__(self):
*/
__pyx_k_tuple_172 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_172)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_172);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_172));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
PyTuple_SET_ITEM(__pyx_k_tuple_172, 0, ((PyObject *)__pyx_kp_s_171));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
@@ -40244,7 +38279,7 @@ static int __Pyx_InitCachedConstants(void) {
* # warning: there could be problems if self.n and self.buf are
*/
__pyx_k_tuple_174 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_174);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_174));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_173));
PyTuple_SET_ITEM(__pyx_k_tuple_174, 0, ((PyObject *)__pyx_kp_s_173));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_173));
@@ -40258,7 +38293,7 @@ static int __Pyx_InitCachedConstants(void) {
* def __str__(self):
*/
__pyx_k_tuple_175 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_175);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_175));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
PyTuple_SET_ITEM(__pyx_k_tuple_175, 0, ((PyObject *)__pyx_kp_s_171));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
@@ -40272,7 +38307,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_180 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_180)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_180);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_180));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_179));
PyTuple_SET_ITEM(__pyx_k_tuple_180, 0, ((PyObject *)__pyx_kp_s_179));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_179));
@@ -40286,7 +38321,7 @@ static int __Pyx_InitCachedConstants(void) {
* except UnicodeDecodeError:
*/
__pyx_k_tuple_181 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_181);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_181));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_181, 0, Py_None);
__Pyx_GIVEREF(Py_None);
@@ -40306,7 +38341,7 @@ static int __Pyx_InitCachedConstants(void) {
* out_stdout = inf.read()
*/
__pyx_k_tuple_182 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_182);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_182));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_182, 0, Py_None);
__Pyx_GIVEREF(Py_None);
@@ -40326,7 +38361,7 @@ static int __Pyx_InitCachedConstants(void) {
* except UnicodeDecodeError:
*/
__pyx_k_tuple_183 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_183);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_183));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_183, 0, Py_None);
__Pyx_GIVEREF(Py_None);
@@ -40346,7 +38381,7 @@ static int __Pyx_InitCachedConstants(void) {
* out_stderr = inf.read()
*/
__pyx_k_tuple_184 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_184);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_184));
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_k_tuple_184, 0, Py_None);
__Pyx_GIVEREF(Py_None);
@@ -40366,132 +38401,12 @@ static int __Pyx_InitCachedConstants(void) {
* #####################################################################
*/
__pyx_k_tuple_252 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_252)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_252);
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_252));
__Pyx_INCREF(((PyObject *)__pyx_kp_s_251));
PyTuple_SET_ITEM(__pyx_k_tuple_252, 0, ((PyObject *)__pyx_kp_s_251));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_251));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_252));
- /* "csamtools.pyx":260
- * list of reads (:class:`pysam.PileupRead`) aligned to this column
- * '''
- * def __str__(self): # <<<<<<<<<<<<<<
- * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
- * "\n" + "\n".join( map(str, self.pileups) )
- */
- __pyx_k_tuple_254 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_254)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_254);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_254, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_254));
- __pyx_k_codeobj_255 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_254, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____str__, 260, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":308
- * stderr is captured.
- * '''
- * def __init__(self): # <<<<<<<<<<<<<<
- * return
- * self.stderr_h, self.stderr_f = tempfile.mkstemp()
- */
- __pyx_k_tuple_258 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_258);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_258, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258));
- __pyx_k_codeobj_259 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_258, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 308, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":314
- * self.stderr_save.setfd( self.stderr_h )
- *
- * def readAndRelease( self ): # <<<<<<<<<<<<<<
- * return []
- * self.stderr_save.restore()
- */
- __pyx_k_tuple_260 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_260)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_260);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_260));
- __pyx_k_codeobj_261 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_260, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__readAndRelease, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_261)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":323
- * return lines
- *
- * def release(self): # <<<<<<<<<<<<<<
- * return
- * self.stderr_save.restore()
- */
- __pyx_k_tuple_262 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_262)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_262);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_262, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_262));
- __pyx_k_codeobj_263 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_262, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__release, 323, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_263)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":329
- * os.remove( self.stderr_f )
- *
- * def __del__(self): # <<<<<<<<<<<<<<
- * self.release()
- *
- */
- __pyx_k_tuple_264 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_264)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_264);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_264, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_264));
- __pyx_k_codeobj_265 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_264, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____del__, 329, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_265)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":334
- * class StderrStoreWindows():
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass # <<<<<<<<<<<<<<
- * def readAndRelease(self): return []
- * def release(self): pass
- */
- __pyx_k_tuple_267 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_267)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_267);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_267, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_267));
- __pyx_k_codeobj_268 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_267, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 334, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_268)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":335
- * '''does nothing. stderr can't be redirected on windows'''
- * def __init__(self): pass
- * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
- * def release(self): pass
- *
- */
- __pyx_k_tuple_269 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_269)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_269);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_269, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_269));
- __pyx_k_codeobj_270 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_269, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__readAndRelease, 335, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_270)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":336
- * def __init__(self): pass
- * def readAndRelease(self): return []
- * def release(self): pass # <<<<<<<<<<<<<<
- *
- * if platform.system()=='Windows':
- */
- __pyx_k_tuple_271 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_271)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_271);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_271, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_271));
- __pyx_k_codeobj_272 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_271, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__release, 336, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_272)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
/* "csamtools.pyx":354
*
* # order of records within sam headers
@@ -40499,302 +38414,146 @@ static int __Pyx_InitCachedConstants(void) {
*
* # type conversions within sam header records
*/
- __pyx_k_tuple_274 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_274)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_274);
+ __pyx_k_tuple_257 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_257)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_257));
__Pyx_INCREF(((PyObject *)__pyx_n_s__HD));
- PyTuple_SET_ITEM(__pyx_k_tuple_274, 0, ((PyObject *)__pyx_n_s__HD));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 0, ((PyObject *)__pyx_n_s__HD));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__HD));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SQ));
- PyTuple_SET_ITEM(__pyx_k_tuple_274, 1, ((PyObject *)__pyx_n_s__SQ));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 1, ((PyObject *)__pyx_n_s__SQ));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SQ));
__Pyx_INCREF(((PyObject *)__pyx_n_s__RG));
- PyTuple_SET_ITEM(__pyx_k_tuple_274, 2, ((PyObject *)__pyx_n_s__RG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 2, ((PyObject *)__pyx_n_s__RG));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__RG));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PG));
- PyTuple_SET_ITEM(__pyx_k_tuple_274, 3, ((PyObject *)__pyx_n_s__PG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 3, ((PyObject *)__pyx_n_s__PG));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PG));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CO));
- PyTuple_SET_ITEM(__pyx_k_tuple_274, 4, ((PyObject *)__pyx_n_s__CO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_257, 4, ((PyObject *)__pyx_n_s__CO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CO));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_274));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_257));
/* "csamtools.pyx":364
*
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
*/
- __pyx_k_tuple_275 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_275)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_275);
+ __pyx_k_tuple_258 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_258));
__Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 0, ((PyObject *)__pyx_n_s__VN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_258, 0, ((PyObject *)__pyx_n_s__VN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SO));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 1, ((PyObject *)__pyx_n_s__SO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_258, 1, ((PyObject *)__pyx_n_s__SO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SO));
__Pyx_INCREF(((PyObject *)__pyx_n_s__GO));
- PyTuple_SET_ITEM(__pyx_k_tuple_275, 2, ((PyObject *)__pyx_n_s__GO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_258, 2, ((PyObject *)__pyx_n_s__GO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__GO));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_275));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258));
/* "csamtools.pyx":365
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
- * "PG" : ( "PN", "ID", "VN", "CL" ), }
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
+ * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*/
- __pyx_k_tuple_276 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_276)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_276);
+ __pyx_k_tuple_259 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_259));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SN));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 0, ((PyObject *)__pyx_n_s__SN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 0, ((PyObject *)__pyx_n_s__SN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__LN));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 1, ((PyObject *)__pyx_n_s__LN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 1, ((PyObject *)__pyx_n_s__LN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__LN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__AS));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 2, ((PyObject *)__pyx_n_s__AS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 2, ((PyObject *)__pyx_n_s__AS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__AS));
__Pyx_INCREF(((PyObject *)__pyx_n_s__M5));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 3, ((PyObject *)__pyx_n_s__M5));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 3, ((PyObject *)__pyx_n_s__M5));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__M5));
__Pyx_INCREF(((PyObject *)__pyx_n_s__UR));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 4, ((PyObject *)__pyx_n_s__UR));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 4, ((PyObject *)__pyx_n_s__UR));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__UR));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SP));
- PyTuple_SET_ITEM(__pyx_k_tuple_276, 5, ((PyObject *)__pyx_n_s__SP));
+ PyTuple_SET_ITEM(__pyx_k_tuple_259, 5, ((PyObject *)__pyx_n_s__SP));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SP));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_276));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_259));
/* "csamtools.pyx":366
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), # <<<<<<<<<<<<<<
- * "PG" : ( "PN", "ID", "VN", "CL" ), }
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), # <<<<<<<<<<<<<<
+ * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*
*/
- __pyx_k_tuple_277 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_277)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_277);
+ __pyx_k_tuple_260 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_260)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_260));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 0, ((PyObject *)__pyx_n_s__ID));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 0, ((PyObject *)__pyx_n_s__ID));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
__Pyx_INCREF(((PyObject *)__pyx_n_s__SM));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 1, ((PyObject *)__pyx_n_s__SM));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 1, ((PyObject *)__pyx_n_s__SM));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__SM));
__Pyx_INCREF(((PyObject *)__pyx_n_s__LB));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 2, ((PyObject *)__pyx_n_s__LB));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 2, ((PyObject *)__pyx_n_s__LB));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__LB));
__Pyx_INCREF(((PyObject *)__pyx_n_s__DS));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 3, ((PyObject *)__pyx_n_s__DS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 3, ((PyObject *)__pyx_n_s__DS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__DS));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PU));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 4, ((PyObject *)__pyx_n_s__PU));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 4, ((PyObject *)__pyx_n_s__PU));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PU));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PI));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 5, ((PyObject *)__pyx_n_s__PI));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 5, ((PyObject *)__pyx_n_s__PI));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PI));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CN));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 6, ((PyObject *)__pyx_n_s__CN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 6, ((PyObject *)__pyx_n_s__CN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__DT));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 7, ((PyObject *)__pyx_n_s__DT));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 7, ((PyObject *)__pyx_n_s__DT));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__DT));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PL));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 8, ((PyObject *)__pyx_n_s__PL));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 8, ((PyObject *)__pyx_n_s__PL));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PL));
__Pyx_INCREF(((PyObject *)__pyx_n_s__FO));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 9, ((PyObject *)__pyx_n_s__FO));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 9, ((PyObject *)__pyx_n_s__FO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__FO));
__Pyx_INCREF(((PyObject *)__pyx_n_s__KS));
- PyTuple_SET_ITEM(__pyx_k_tuple_277, 10, ((PyObject *)__pyx_n_s__KS));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 10, ((PyObject *)__pyx_n_s__KS));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__KS));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_277));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__PG));
+ PyTuple_SET_ITEM(__pyx_k_tuple_260, 11, ((PyObject *)__pyx_n_s__PG));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PG));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_260));
/* "csamtools.pyx":367
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
- * "PG" : ( "PN", "ID", "VN", "CL" ), } # <<<<<<<<<<<<<<
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
+ * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<<
*
*
*/
- __pyx_k_tuple_278 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_278)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_278);
+ __pyx_k_tuple_261 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_261)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_261));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PN));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 0, ((PyObject *)__pyx_n_s__PN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 0, ((PyObject *)__pyx_n_s__PN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 1, ((PyObject *)__pyx_n_s__ID));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 1, ((PyObject *)__pyx_n_s__ID));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
__Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 2, ((PyObject *)__pyx_n_s__VN));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 2, ((PyObject *)__pyx_n_s__VN));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
__Pyx_INCREF(((PyObject *)__pyx_n_s__CL));
- PyTuple_SET_ITEM(__pyx_k_tuple_278, 3, ((PyObject *)__pyx_n_s__CL));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 3, ((PyObject *)__pyx_n_s__CL));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__CL));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_278));
-
- /* "csamtools.pyx":3092
- * class Outs:
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1): # <<<<<<<<<<<<<<
- * self.streams = []
- * self.id = id
- */
- __pyx_k_tuple_279 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_279)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_279);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_279, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__id));
- PyTuple_SET_ITEM(__pyx_k_tuple_279, 1, ((PyObject *)__pyx_n_s__id));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__id));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_279));
- __pyx_k_codeobj_280 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_279, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s____init__, 3092, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_280)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_k_tuple_281 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_281)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_281);
- __Pyx_INCREF(((PyObject *)__pyx_int_1));
- PyTuple_SET_ITEM(__pyx_k_tuple_281, 0, ((PyObject *)__pyx_int_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_int_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_281));
-
- /* "csamtools.pyx":3096
- * self.id = id
- *
- * def setdevice(self, filename): # <<<<<<<<<<<<<<
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY)
- */
- __pyx_k_tuple_282 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_282)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_282);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_282, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
- PyTuple_SET_ITEM(__pyx_k_tuple_282, 1, ((PyObject *)__pyx_n_s__filename));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
- PyTuple_SET_ITEM(__pyx_k_tuple_282, 2, ((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_282));
- __pyx_k_codeobj_283 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_282, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setdevice, 3096, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_283)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":3101
- * self.setfd(fd)
- *
- * def setfile(self, filename): # <<<<<<<<<<<<<<
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
- */
- __pyx_k_tuple_284 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_284)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_284);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_284, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
- PyTuple_SET_ITEM(__pyx_k_tuple_284, 1, ((PyObject *)__pyx_n_s__filename));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
- PyTuple_SET_ITEM(__pyx_k_tuple_284, 2, ((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_284));
- __pyx_k_codeobj_285 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_284, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setfile, 3101, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_285)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":3106
- * self.setfd(fd)
- *
- * def setfd(self, fd): # <<<<<<<<<<<<<<
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd)
- */
- __pyx_k_tuple_286 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_286)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_286);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_286, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fd));
- PyTuple_SET_ITEM(__pyx_k_tuple_286, 1, ((PyObject *)__pyx_n_s__fd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ofd));
- PyTuple_SET_ITEM(__pyx_k_tuple_286, 2, ((PyObject *)__pyx_n_s__ofd));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ofd));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_286));
- __pyx_k_codeobj_287 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_286, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__setfd, 3106, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_287)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":3114
- * os.close(fd) # Close other unit (look out, caller.)
- *
- * def restore(self): # <<<<<<<<<<<<<<
- * '''restore previous output stream'''
- * if self.streams:
- */
- __pyx_k_tuple_288 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_288)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_288);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_288, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_288));
- __pyx_k_codeobj_289 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_288, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s__restore, 3114, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_289)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":3125
- * del self.streams[-1]
- *
- * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
- * args = (),
- * catch_stdout = True ):
- */
- __pyx_k_tuple_291 = PyTuple_New(16); if (unlikely(!__pyx_k_tuple_291)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_291);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__method));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 0, ((PyObject *)__pyx_n_s__method));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__method));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__args));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 1, ((PyObject *)__pyx_n_s__args));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__args));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__catch_stdout));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 2, ((PyObject *)__pyx_n_s__catch_stdout));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__catch_stdout));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stderr_h));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 3, ((PyObject *)__pyx_n_s__stderr_h));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stderr_h));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stderr_f));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 4, ((PyObject *)__pyx_n_s__stderr_f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stderr_f));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_h));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 5, ((PyObject *)__pyx_n_s__stdout_h));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_h));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_f));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 6, ((PyObject *)__pyx_n_s__stdout_f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_f));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stdout_save));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 7, ((PyObject *)__pyx_n_s__stdout_save));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stdout_save));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__cargs));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 8, ((PyObject *)__pyx_n_s__cargs));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cargs));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 9, ((PyObject *)__pyx_n_s__i));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 10, ((PyObject *)__pyx_n_s__n));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__retval));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 11, ((PyObject *)__pyx_n_s__retval));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__retval));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__inf));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 12, ((PyObject *)__pyx_n_s__inf));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__inf));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__out_stdout));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 13, ((PyObject *)__pyx_n_s__out_stdout));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__out_stdout));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__out_stderr));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 14, ((PyObject *)__pyx_n_s__out_stderr));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__out_stderr));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__a));
- PyTuple_SET_ITEM(__pyx_k_tuple_291, 15, ((PyObject *)__pyx_n_s__a));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__a));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_291));
- __pyx_k_codeobj_292 = (PyObject*)__Pyx_PyCode_New(3, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_291, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_256, __pyx_n_s___samtools_dispatch, 3125, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_292)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__PP));
+ PyTuple_SET_ITEM(__pyx_k_tuple_261, 4, ((PyObject *)__pyx_n_s__PP));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PP));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_261));
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -40853,18 +38612,12 @@ PyMODINIT_FUNC PyInit_csamtools(void)
Py_FatalError("failed to import 'refnanny' module");
}
#endif
- __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)", 0);
+ __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)");
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;}
- #ifdef __Pyx_CyFunction_USED
- if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- #ifdef __Pyx_FusedFunction_USED
- if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #endif
- #ifdef __Pyx_Generator_USED
- 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;}
#endif
/*--- Library function declarations ---*/
/*--- Threads initialization code ---*/
@@ -40910,9 +38663,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_11AlignedRead_4__str__.doc = __pyx_doc_9csamtools_11AlignedRead_4__str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_4__str__;
+ __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__.doc = __pyx_doc_9csamtools_11AlignedRead_2__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_2__str__;
}
}
if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -40927,9 +38680,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_7Samfile_42__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_7Samfile_42__next__.doc = __pyx_doc_9csamtools_7Samfile_42__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_42__next__;
+ __pyx_wrapperbase_9csamtools_7Samfile_21__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_7Samfile_21__next__.doc = __pyx_doc_9csamtools_7Samfile_21__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_21__next__;
}
}
if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -40952,9 +38705,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_4__next__;
+ __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__;
}
}
if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -40968,9 +38721,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_4__next__;
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__;
}
}
if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -40981,9 +38734,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_6__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_6__next__;
+ __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
}
}
if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -40996,9 +38749,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_4__next__;
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__;
}
}
if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41021,9 +38774,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_2__next__;
+ __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__;
}
}
if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41036,9 +38789,9 @@ PyMODINIT_FUNC PyInit_csamtools(void)
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_2__next__;
+ __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__;
}
}
if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41050,8 +38803,12 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
+ if (PyType_Ready(&__pyx_Generator_type) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_9csamtools___pyx_Generator = &__pyx_Generator_type;
+ __pyx_type_9csamtools___pyx_scope_struct__genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator;
if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_9csamtools___pyx_scope_struct__genexpr;
+ __pyx_type_9csamtools___pyx_scope_struct_1_genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator;
if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_9csamtools___pyx_scope_struct_1_genexpr;
/*--- Type import code ---*/
@@ -41317,10 +39074,10 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
- __pyx_t_1 = __pyx_pf_9csamtools_2genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_pf_9csamtools_1genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -41340,10 +39097,10 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
*
*/
- __pyx_t_1 = __pyx_pf_9csamtools_5genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_pf_9csamtools_3genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -41417,7 +39174,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) )
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_12PileupColumn_1__str__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_255)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_12PileupColumn___str__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____str__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -41430,11 +39187,11 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* all the reads that map to a certain target base.
*/
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_INCREF(__pyx_builtin_object);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_builtin_object);
__Pyx_GIVEREF(__pyx_builtin_object);
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_257)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_254)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -41459,7 +39216,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* return
* self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_259)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41471,7 +39228,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* return []
* self.stderr_save.restore()
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_3readAndRelease, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_261)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41483,7 +39240,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* return
* self.stderr_save.restore()
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_5release, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_263)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41495,7 +39252,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* self.release()
*
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_11StderrStore_7__del__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_265)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_3__del__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____del__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41507,7 +39264,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* '''
* stderr is captured.
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_266)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_255)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41531,7 +39288,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* def readAndRelease(self): return []
* def release(self): pass
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_268)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41543,7 +39300,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* def release(self): pass
*
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_3readAndRelease, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_270)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41555,7 +39312,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*
* if platform.system()=='Windows':
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_5release, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_272)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41567,7 +39324,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_273)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_256)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStoreWindows, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41673,7 +39430,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*
* # type conversions within sam header records
*/
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_274)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_257)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":357
*
@@ -41697,7 +39454,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, # <<<<<<<<<<<<<<
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
- * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str },
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
*/
__pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
@@ -41714,8 +39471,8 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, # <<<<<<<<<<<<<<
- * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str },
- * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, }
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
+ * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, }
*/
__pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
@@ -41729,8 +39486,8 @@ PyMODINIT_FUNC PyInit_csamtools(void)
/* "csamtools.pyx":360
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
- * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str }, # <<<<<<<<<<<<<<
- * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, }
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, # <<<<<<<<<<<<<<
+ * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, }
*
*/
if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41738,13 +39495,14 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__FO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__KS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
/* "csamtools.pyx":361
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
- * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str },
- * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, } # <<<<<<<<<<<<<<
+ * "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
+ * "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } # <<<<<<<<<<<<<<
*
* # output order of fields within records
*/
@@ -41754,6 +39512,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41764,38 +39523,38 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
*/
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_275)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_258)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":365
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
- * "PG" : ( "PN", "ID", "VN", "CL" ), }
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
+ * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_276)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_259)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":366
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ), # <<<<<<<<<<<<<<
- * "PG" : ( "PN", "ID", "VN", "CL" ), }
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), # <<<<<<<<<<<<<<
+ * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_277)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_260)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "csamtools.pyx":367
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
- * "PG" : ( "PN", "ID", "VN", "CL" ), } # <<<<<<<<<<<<<<
+ * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
+ * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<<
*
*
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_278)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_261)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -41890,9 +39649,8 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* self.streams = []
* self.id = id
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_1__init__, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_280)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_4, ((PyObject *)__pyx_k_tuple_281));
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41903,7 +39661,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY)
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_3setdevice, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_283)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_1setdevice, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setdevice, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41915,7 +39673,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_5setfile, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_285)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_2setfile, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfile, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41927,7 +39685,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd)
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_7setfd, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_287)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_3setfd, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfd, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41939,7 +39697,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* '''restore previous output stream'''
* if self.streams:
*/
- __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_9csamtools_4Outs_9restore, 0, NULL, __pyx_n_s__csamtools, ((PyObject *)__pyx_k_codeobj_289)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_4restore, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__restore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -41951,7 +39709,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1):
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_290)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_262)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__Outs, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -41978,7 +39736,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* args = (),
* catch_stdout = True ):
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9csamtools_1_samtools_dispatch, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9csamtools__samtools_dispatch, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -41991,7 +39749,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* "IteratorRow",
*/
__pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_INCREF(((PyObject *)__pyx_n_s__Samfile));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Samfile));
@@ -42052,6 +39810,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
/* Runtime support code */
+
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
PyObject *m = NULL, *p = NULL;
@@ -42083,7 +39842,9 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
return result;
}
+
#if CYTHON_PROFILE
+
static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
PyFrameObject** frame,
const char *funcname,
@@ -42107,10 +39868,12 @@ static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
}
return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
}
+
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
PyCodeObject *py_code = 0;
+
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
py_srcfile = PyString_FromString(srcfile);
@@ -42119,6 +39882,7 @@ static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const cha
py_srcfile = PyUnicode_FromString(srcfile);
#endif
if (!py_funcname | !py_srcfile) goto bad;
+
py_code = PyCode_New(
0, /*int argcount,*/
#if PY_MAJOR_VERSION >= 3
@@ -42138,17 +39902,20 @@ static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const cha
firstlineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
+
bad:
Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
+
return py_code;
}
+
#endif /* CYTHON_PROFILE */
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
+
tmp_type = tstate->curexc_type;
tmp_value = tstate->curexc_value;
tmp_tb = tstate->curexc_traceback;
@@ -42158,30 +39925,27 @@ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyOb
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
}
+
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->curexc_type;
*value = tstate->curexc_value;
*tb = tstate->curexc_traceback;
+
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
}
+
#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ /* cause is unused */
Py_XINCREF(type);
Py_XINCREF(value);
Py_XINCREF(tb);
+ /* First, check the traceback argument, replacing None with NULL. */
if (tb == Py_None) {
Py_DECREF(tb);
tb = 0;
@@ -42191,6 +39955,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
"raise: arg 3 must be a traceback or None");
goto raise_error;
}
+ /* Next, replace a missing value with None */
if (value == NULL) {
value = Py_None;
Py_INCREF(value);
@@ -42201,11 +39966,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
if (!PyType_Check(type))
#endif
{
+ /* Raising an instance. The value should be a dummy. */
if (value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
+ /* Normalize to raise <class>, <instance> */
Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
@@ -42229,6 +39996,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
}
#endif
}
+
__Pyx_ErrRestore(type, value, tb);
return;
raise_error:
@@ -42237,7 +40005,9 @@ raise_error:
Py_XDECREF(tb);
return;
}
+
#else /* Python 3+ */
+
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
if (tb == Py_None) {
tb = 0;
@@ -42248,6 +40018,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
if (value == Py_None)
value = 0;
+
if (PyExceptionInstance_Check(type)) {
if (value) {
PyErr_SetString(PyExc_TypeError,
@@ -42261,6 +40032,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"raise: exception class must be a subclass of BaseException");
goto bad;
}
+
if (cause) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
@@ -42283,7 +40055,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
PyException_SetCause(value, fixed_cause);
}
+
PyErr_SetObject(type, value);
+
if (tb) {
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
@@ -42293,6 +40067,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
Py_XDECREF(tmp_tb);
}
}
+
bad:
return;
}
@@ -42321,7 +40096,7 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
#else
- if (unlikely(!PyUnicode_Check(key)))
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
#endif
goto invalid_keyword_type;
}
@@ -42369,6 +40144,7 @@ static int __Pyx_ParseOptionalKeywords(
Py_ssize_t pos = 0;
PyObject*** name;
PyObject*** first_kw_arg = argnames + num_pos_args;
+
while (PyDict_Next(kwds, &pos, &key, &value)) {
name = first_kw_arg;
while (*name && (**name != key)) name++;
@@ -42378,7 +40154,7 @@ static int __Pyx_ParseOptionalKeywords(
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
#else
- if (unlikely(!PyUnicode_Check(key))) {
+ if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
#endif
goto invalid_keyword_type;
} else {
@@ -42394,6 +40170,7 @@ static int __Pyx_ParseOptionalKeywords(
if (*name) {
values[name-argnames] = value;
} else {
+ /* unexpected keyword found */
for (name=argnames; name != first_kw_arg; name++) {
if (**name == key) goto arg_passed_twice;
#if PY_MAJOR_VERSION >= 3
@@ -42443,6 +40220,7 @@ static void __Pyx_RaiseArgtupleInvalid(
{
Py_ssize_t num_expected;
const char *more_or_less;
+
if (num_found < num_min) {
num_expected = num_min;
more_or_less = "at least";
@@ -42575,7 +40353,6 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
}
-
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
@@ -42585,6 +40362,7 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*value);
Py_XINCREF(*tb);
}
+
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
@@ -42625,33 +40403,12 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
goto bad;
#if PY_VERSION_HEX >= 0x02050000
{
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- /* try package relative import first */
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- }
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
}
#else
if (level>0) {
@@ -42698,8 +40455,10 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
PyObject *modname) {
PyObject *result;
PyObject *metaclass;
+
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
+
/* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
@@ -42712,367 +40471,48 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
return result;
}
-static PyObject *
-__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
-{
- if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
-#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
-#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
-#endif
- }
- if (op->func_doc == 0) {
- Py_INCREF(Py_None);
- return Py_None;
- }
- Py_INCREF(op->func_doc);
- return op->func_doc;
-}
-static int
-__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp = op->func_doc;
- if (value == NULL)
- op->func_doc = Py_None; /* Mark as deleted */
- else
- op->func_doc = value;
- Py_INCREF(op->func_doc);
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
-{
- if (op->func_name == NULL) {
-#if PY_MAJOR_VERSION >= 3
- op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
-#else
- op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
-#endif
- }
- Py_INCREF(op->func_name);
- return op->func_name;
-}
-static int
-__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (value == NULL || !PyUnicode_Check(value)) {
-#else
- if (value == NULL || !PyString_Check(value)) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__name__ must be set to a string object");
- return -1;
- }
- tmp = op->func_name;
- Py_INCREF(value);
- op->func_name = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
-{
- PyObject *self;
- self = m->func_closure;
- if (self == NULL)
- self = Py_None;
- Py_INCREF(self);
- return self;
-}
-static PyObject *
-__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
-{
- if (op->func_dict == NULL) {
- op->func_dict = PyDict_New();
- if (op->func_dict == NULL)
- return NULL;
- }
- Py_INCREF(op->func_dict);
- return op->func_dict;
-}
-static int
-__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
- if (value == NULL) {
- PyErr_SetString(PyExc_TypeError,
- "function's dictionary may not be deleted");
- return -1;
- }
- if (!PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "setting function's dictionary to a non-dict");
- return -1;
- }
- tmp = op->func_dict;
- Py_INCREF(value);
- op->func_dict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- PyObject* dict = PyModule_GetDict(__pyx_m);
- Py_XINCREF(dict);
- return dict;
-}
-static PyObject *
-__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyObject *
-__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
-{
- PyObject* result = (op->func_code) ? op->func_code : Py_None;
- Py_INCREF(result);
- return result;
-}
-static PyObject *
-__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
-{
- if (op->defaults_tuple) {
- Py_INCREF(op->defaults_tuple);
- return op->defaults_tuple;
- }
- if (op->defaults_getter) {
- PyObject *res = op->defaults_getter((PyObject *) op);
- if (res) {
- Py_INCREF(res);
- op->defaults_tuple = res;
- }
- return res;
- }
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyGetSetDef __pyx_CyFunction_getsets[] = {
- {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
- {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
- {0, 0, 0, 0, 0}
-};
-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
-#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
-#endif
-static PyMemberDef __pyx_CyFunction_members[] = {
- {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
- {0, 0, 0, 0, 0}
-};
-static PyObject *
-__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromString(m->func.m_ml->ml_name);
-#else
- return PyString_FromString(m->func.m_ml->ml_name);
-#endif
-}
-static PyMethodDef __pyx_CyFunction_methods[] = {
- {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
- {0, 0, 0, 0}
-};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
- PyObject *closure, PyObject *module, PyObject* code) {
- __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
+
+static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
+ __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
if (op == NULL)
return NULL;
- op->flags = flags;
- op->func_weakreflist = NULL;
op->func.m_ml = ml;
- op->func.m_self = (PyObject *) op;
- Py_XINCREF(closure);
- op->func_closure = closure;
+ Py_XINCREF(self);
+ op->func.m_self = self;
Py_XINCREF(module);
op->func.m_module = module;
- op->func_dict = NULL;
- op->func_name = NULL;
- op->func_doc = NULL;
- op->func_classobj = NULL;
- Py_XINCREF(code);
- op->func_code = code;
- op->defaults_pyobjects = 0;
- op->defaults = NULL;
- op->defaults_tuple = NULL;
- op->defaults_getter = NULL;
PyObject_GC_Track(op);
- return (PyObject *) op;
-}
-static int
-__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
-{
- Py_CLEAR(m->func_closure);
- Py_CLEAR(m->func.m_module);
- Py_CLEAR(m->func_dict);
- Py_CLEAR(m->func_name);
- Py_CLEAR(m->func_doc);
- Py_CLEAR(m->func_code);
- Py_CLEAR(m->func_classobj);
- Py_CLEAR(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_XDECREF(pydefaults[i]);
- PyMem_Free(m->defaults);
- m->defaults = NULL;
- }
- return 0;
+ return (PyObject *)op;
}
-static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
-{
+
+static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
PyObject_GC_UnTrack(m);
- if (m->func_weakreflist != NULL)
- PyObject_ClearWeakRefs((PyObject *) m);
- __Pyx_CyFunction_clear(m);
+ Py_XDECREF(m->func.m_self);
+ Py_XDECREF(m->func.m_module);
PyObject_GC_Del(m);
}
-static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
-{
- Py_VISIT(m->func_closure);
- Py_VISIT(m->func.m_module);
- Py_VISIT(m->func_dict);
- Py_VISIT(m->func_name);
- Py_VISIT(m->func_doc);
- Py_VISIT(m->func_code);
- Py_VISIT(m->func_classobj);
- Py_VISIT(m->defaults_tuple);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_VISIT(pydefaults[i]);
- }
- return 0;
-}
-static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
- Py_INCREF(func);
- return func;
- }
- if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
- if (type == NULL)
- type = (PyObject *)(Py_TYPE(obj));
- return PyMethod_New(func,
- type, (PyObject *)(Py_TYPE(type)));
- }
+
+static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
if (obj == Py_None)
- obj = NULL;
+ obj = NULL;
return PyMethod_New(func, obj, type);
}
-static PyObject*
-__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
-{
- PyObject *func_name = __Pyx_CyFunction_get_name(op);
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromFormat("<cyfunction %U at %p>",
- func_name, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(func_name), (void *)op);
-#endif
-}
-static PyTypeObject __pyx_CyFunctionType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
- sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- __Pyx_PyCFunction_Call, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
- (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_CyFunction_methods, /*tp_methods*/
- __pyx_CyFunction_members, /*tp_members*/
- __pyx_CyFunction_getsets, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- __Pyx_CyFunction_descr_get, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-};
-static int __Pyx_CyFunction_init(void)
-{
- if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
+
+static int __pyx_binding_PyCFunctionType_init(void) {
+ __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
+ __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
+ __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
+ __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
+ if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
return -1;
- __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
+ }
+ __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
return 0;
-}
-void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, sizeof(size));
- m->defaults_pyobjects = pyobjects;
- return m->defaults;
-}
-static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
+
}
static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
+ if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
return (equals == Py_EQ);
} else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
@@ -43102,26 +40542,16 @@ static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int eq
}
static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
+ if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
return (equals == Py_EQ);
} else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
return (equals == Py_NE);
} else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
+ if (equals == Py_EQ)
+ return (PyUnicode_AS_UNICODE(s1)[0] == PyUnicode_AS_UNICODE(s2)[0]);
+ else
+ return (PyUnicode_AS_UNICODE(s1)[0] != PyUnicode_AS_UNICODE(s2)[0]);
} else {
int result = PyUnicode_Compare(s1, s2);
if ((result == -1) && unlikely(PyErr_Occurred()))
@@ -43954,79 +41384,86 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
+
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
+
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
+
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
}
-static PyObject *__Pyx_Generator_Next(PyObject *self);
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
-static PyObject *__Pyx_Generator_Close(PyObject *self);
-static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
-static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
+static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self)
{
- PyObject *exc_type = self->exc_type;
- PyObject *exc_value = self->exc_value;
- PyObject *exc_traceback = self->exc_traceback;
+ Py_XDECREF(self->exc_type);
+ Py_XDECREF(self->exc_value);
+ Py_XDECREF(self->exc_traceback);
+
self->exc_type = NULL;
self->exc_value = NULL;
self->exc_traceback = NULL;
- Py_XDECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_traceback);
}
-static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
+
+static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value)
{
PyObject *retval;
- if (unlikely(self->is_running)) {
+
+ if (self->is_running) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
return NULL;
}
- if (unlikely(self->resume_label == 0)) {
- if (unlikely(value && value != Py_None)) {
+
+ if (self->resume_label == 0) {
+ if (value && value != Py_None) {
PyErr_SetString(PyExc_TypeError,
"can't send non-None value to a "
"just-started generator");
return NULL;
}
}
- if (unlikely(self->resume_label == -1)) {
+
+ if (self->resume_label == -1) {
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
+
+
if (value)
__Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
else
__Pyx_Generator_ExceptionClear(self);
+
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
+
if (retval)
__Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
else
__Pyx_Generator_ExceptionClear(self);
+
return retval;
}
+
static PyObject *__Pyx_Generator_Next(PyObject *self)
{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None);
}
+
static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
+ return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value);
}
+
static PyObject *__Pyx_Generator_Close(PyObject *self)
{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
PyObject *retval;
#if PY_VERSION_HEX < 0x02050000
PyErr_SetNone(PyExc_StopIteration);
@@ -44053,190 +41490,19 @@ static PyObject *__Pyx_Generator_Close(PyObject *self)
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
+
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds)
{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+ struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
+
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
__Pyx_Raise(typ, val, tb, NULL);
return __Pyx_Generator_SendEx(generator, NULL);
}
-static int
-__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
-{
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_VISIT(gen->closure);
- Py_VISIT(gen->classobj);
- Py_VISIT(gen->exc_type);
- Py_VISIT(gen->exc_value);
- Py_VISIT(gen->exc_traceback);
- return 0;
-}
-static void
-__Pyx_Generator_dealloc(PyObject *self)
-{
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject_GC_UnTrack(gen);
- if (gen->gi_weakreflist != NULL)
- PyObject_ClearWeakRefs(self);
- PyObject_GC_Track(self);
- if (gen->resume_label > 0) {
- Py_TYPE(gen)->tp_del(self);
- if (self->ob_refcnt > 0)
- return; /* resurrected. :( */
- }
- PyObject_GC_UnTrack(self);
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- PyObject_GC_Del(gen);
-}
-static void
-__Pyx_Generator_del(PyObject *self)
-{
- PyObject *res;
- PyObject *error_type, *error_value, *error_traceback;
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- if (gen->resume_label <= 0)
- return ;
- assert(self->ob_refcnt == 0);
- self->ob_refcnt = 1;
- __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
- res = __Pyx_Generator_Close(self);
- if (res == NULL)
- PyErr_WriteUnraisable(self);
- else
- Py_DECREF(res);
- __Pyx_ErrRestore(error_type, error_value, error_traceback);
- /* Undo the temporary resurrection; can't use DECREF here, it would
- * cause a recursive call.
- */
- assert(self->ob_refcnt > 0);
- if (--self->ob_refcnt == 0)
- return; /* this is the normal path out */
- /* close() resurrected it! Make it look like the original Py_DECREF
- * never happened.
- */
- {
- Py_ssize_t refcnt = self->ob_refcnt;
- _Py_NewReference(self);
- self->ob_refcnt = refcnt;
- }
- assert(PyType_IS_GC(self->ob_type) &&
- _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
- /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
- * we need to undo that. */
- _Py_DEC_REFTOTAL;
- /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
- * chain, so no more to do there.
- * If COUNT_ALLOCS, the original decref bumped tp_frees, and
- * _Py_NewReference bumped tp_allocs: both of those need to be
- * undone.
- */
-#ifdef COUNT_ALLOCS
- --self->ob_type->tp_frees;
- --self->ob_type->tp_allocs;
-#endif
-}
-static PyMemberDef __pyx_Generator_memberlist[] = {
- {(char *) "gi_running",
- T_INT,
- offsetof(__pyx_GeneratorObject, is_running),
- READONLY,
- NULL},
- {0, 0, 0, 0, 0}
-};
-static PyMethodDef __pyx_Generator_methods[] = {
- {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
- {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
- {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
- {0, 0, 0, 0}
-};
-static PyTypeObject __pyx_GeneratorType = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("generator"), /*tp_name*/
- sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- PyObject_GenericGetAttr, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- PyObject_SelfIter, /*tp_iter*/
- (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
- __pyx_Generator_methods, /*tp_methods*/
- __pyx_Generator_memberlist, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- __Pyx_Generator_del, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-};
-static
-__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure)
-{
- __pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
- if (gen == NULL)
- return NULL;
- gen->body = body;
- gen->closure = closure;
- Py_XINCREF(closure);
- gen->is_running = 0;
- gen->resume_label = 0;
- gen->classobj = NULL;
- gen->exc_type = NULL;
- gen->exc_value = NULL;
- gen->exc_traceback = NULL;
- gen->gi_weakreflist = NULL;
- PyObject_GC_Track(gen);
- return gen;
-}
-static int __pyx_Generator_init(void)
-{
- return PyType_Ready(&__pyx_GeneratorType);
-}
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename) {
@@ -44302,10 +41568,15 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
+
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(class_name);
+ #else
+ py_name = PyUnicode_FromString(class_name);
+ #endif
if (!py_name)
goto bad;
result = PyObject_GetAttr(py_module, py_name);
@@ -44321,7 +41592,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
module_name, class_name);
goto bad;
}
- if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+ if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
@@ -44331,7 +41602,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
@@ -44350,7 +41621,12 @@ bad:
static PyObject *__Pyx_ImportModule(const char *name) {
PyObject *py_name = 0;
PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
+
+ #if PY_MAJOR_VERSION < 3
+ py_name = PyString_FromString(name);
+ #else
+ py_name = PyUnicode_FromString(name);
+ #endif
if (!py_name)
goto bad;
py_module = PyImport_Import(py_name);
@@ -44362,105 +41638,29 @@ bad:
}
#endif
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
+
+static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
+ int __pyx_lineno, const char *__pyx_filename) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
+ PyObject *py_globals = 0;
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+
#if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
+ py_srcfile = PyString_FromString(__pyx_filename);
#else
- py_srcfile = PyUnicode_FromString(filename);
+ py_srcfile = PyUnicode_FromString(__pyx_filename);
#endif
if (!py_srcfile) goto bad;
- if (c_line) {
+ if (__pyx_clineno) {
#if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
#endif
}
else {
@@ -44471,45 +41671,28 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
#endif
}
if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
+ py_code = PyCode_New(
0, /*int argcount,*/
+ #if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
+ #endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
+ __pyx_lineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
+ if (!py_code) goto bad;
py_frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate,*/
py_code, /*PyCodeObject *code,*/
@@ -44517,9 +41700,11 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
+ py_frame->f_lineno = __pyx_lineno;
PyTraceBack_Here(py_frame);
bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
@@ -44554,7 +41739,6 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-
/* Type Conversion Functions */
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
diff --git a/pysam/csamtools.pyx b/pysam/csamtools.pyx
index 7dd075c..e300c66 100644
--- a/pysam/csamtools.pyx
+++ b/pysam/csamtools.pyx
@@ -357,14 +357,14 @@ VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" )
VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
"SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
"RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
- "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str },
- "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str }, }
+ "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
+ "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, }
# output order of fields within records
VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
"SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
- "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS" ),
- "PG" : ( "PN", "ID", "VN", "CL" ), }
+ "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
+ "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
######################################################################
diff --git a/pysam/ctabix.c b/pysam/ctabix.c
index 9ab49e7..005213c 100644
--- a/pysam/ctabix.c
+++ b/pysam/ctabix.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.17.1 on Tue Nov 20 16:47:00 2012 */
+/* Generated by Cython 0.17.4 on Mon Jan 14 21:45:57 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -53,12 +53,15 @@
(PyErr_Format(PyExc_TypeError, \
"expected index value, got %.200s", Py_TYPE(o)->tp_name), \
(PyObject*)0))
- #define PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && !PyComplex_Check(o))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
#define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
@@ -355,21 +358,21 @@ static const char *__pyx_f[] = {
/*--- Type declarations ---*/
struct __pyx_obj_6ctabix_Parser;
-struct __pyx_obj_6ctabix_asVCF;
+struct __pyx_obj_6ctabix_asGTF;
+struct __pyx_obj_6ctabix_Tabixfile;
struct __pyx_obj_10TabProxies_TupleProxy;
struct __pyx_obj_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_10TabProxies_BedProxy;
-struct __pyx_obj_6ctabix_tabix_copy_iterator;
struct __pyx_obj_10TabProxies_VCFProxy;
-struct __pyx_obj_10TabProxies_GTFProxy;
-struct __pyx_obj_6ctabix_TabixIterator;
+struct __pyx_obj_6ctabix_tabix_inplace_iterator;
+struct __pyx_obj_6ctabix_tabix_copy_iterator;
struct __pyx_obj_6ctabix_TabixIteratorParsed;
+struct __pyx_obj_10TabProxies_BedProxy;
struct __pyx_obj_6ctabix_TabixHeaderIterator;
-struct __pyx_obj_6ctabix_Tabixfile;
-struct __pyx_obj_6ctabix_asGTF;
-struct __pyx_obj_6ctabix_asBed;
-struct __pyx_obj_6ctabix_tabix_inplace_iterator;
struct __pyx_obj_6ctabix_asTuple;
+struct __pyx_obj_10TabProxies_GTFProxy;
+struct __pyx_obj_6ctabix_asBed;
+struct __pyx_obj_6ctabix_TabixIterator;
+struct __pyx_obj_6ctabix_asVCF;
/* "ctabix.pxd":190
* cdef tabix_t * tabixfile
@@ -383,18 +386,33 @@ struct __pyx_obj_6ctabix_Parser {
};
-/* "ctabix.pxd":202
+/* "ctabix.pxd":196
* pass
*
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_6ctabix_asVCF {
+struct __pyx_obj_6ctabix_asGTF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
+/* "ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+ *
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ *
+ * # pointer to tabixfile
+ */
+struct __pyx_obj_6ctabix_Tabixfile {
+ PyObject_HEAD
+ tabix_t *tabixfile;
+ int isremote;
+ char *_filename;
+};
+
+
/* "TabProxies.pxd":41
* ctypedef int uint64_t
*
@@ -427,37 +445,6 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy {
};
-/* "TabProxies.pxd":72
- * pass
- *
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_10TabProxies_BedProxy {
- struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
-};
-
-
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
- *
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
- */
-struct __pyx_obj_6ctabix_tabix_copy_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab;
- FILE *infile;
- struct __pyx_obj_6ctabix_Parser *parser;
-};
-
-
/* "TabProxies.pxd":83
* cdef update( self, char * buffer, size_t nbytes )
*
@@ -472,31 +459,35 @@ struct __pyx_obj_10TabProxies_VCFProxy {
};
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+/* "ctabix.pxd":210
+ * cdef Parser parser
*
- * cdef:
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
*/
-struct __pyx_obj_10TabProxies_GTFProxy {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
+struct __pyx_obj_6ctabix_tabix_inplace_iterator {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab;
+ FILE *infile;
+ char *buffer;
+ size_t size;
+ struct __pyx_obj_6ctabix_Parser *parser;
};
-/* "ctabix.pxd":182
- * cdef char * _filename
+/* "ctabix.pxd":218
+ * cdef __cnext__(self)
*
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef Parser parser
*/
-struct __pyx_obj_6ctabix_TabixIterator {
+struct __pyx_obj_6ctabix_tabix_copy_iterator {
PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
+ struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab;
+ FILE *infile;
+ struct __pyx_obj_6ctabix_Parser *parser;
};
@@ -515,6 +506,22 @@ struct __pyx_obj_6ctabix_TabixIteratorParsed {
};
+/* "TabProxies.pxd":72
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
+ */
+struct __pyx_obj_10TabProxies_BedProxy {
+ struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
+};
+
+
/* "ctabix.pxd":186
* cdef tabix_t * tabixfile
*
@@ -529,30 +536,29 @@ struct __pyx_obj_6ctabix_TabixHeaderIterator {
};
-/* "ctabix.pxd":172
- * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+/* "ctabix.pxd":193
+ * pass
*
- * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * # pointer to tabixfile
*/
-struct __pyx_obj_6ctabix_Tabixfile {
- PyObject_HEAD
- tabix_t *tabixfile;
- int isremote;
- char *_filename;
+struct __pyx_obj_6ctabix_asTuple {
+ struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pxd":196
- * pass
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * pass
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_obj_6ctabix_asGTF {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_10TabProxies_GTFProxy {
+ struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
};
@@ -568,50 +574,33 @@ struct __pyx_obj_6ctabix_asBed {
};
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "ctabix.pxd":182
+ * cdef char * _filename
*
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
+ * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_6ctabix_tabix_inplace_iterator {
+struct __pyx_obj_6ctabix_TabixIterator {
PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab;
- FILE *infile;
- char *buffer;
- size_t size;
- struct __pyx_obj_6ctabix_Parser *parser;
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "ctabix.pxd":193
+/* "ctabix.pxd":202
* pass
*
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_6ctabix_asTuple {
+struct __pyx_obj_6ctabix_asVCF {
struct __pyx_obj_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pyx":768
- * return self.__cnext__()
- *
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * '''iterate over ``infile``.
- *
- */
-
-struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *);
-};
-static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator;
-
-
/* "TabProxies.pxd":41
* ctypedef int uint64_t
*
@@ -644,18 +633,32 @@ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
+/* "TabProxies.pxd":72
+ * pass
*
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_VCFProxy {
+struct __pyx_vtabstruct_10TabProxies_BedProxy {
struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
+
+
+/* "ctabix.pyx":709
+ * ## Iterators for parsing through unindexed files.
+ * #########################################################
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
+ *
+ */
+
+struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *);
+};
+static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator;
/* "TabProxies.pxd":60
@@ -673,32 +676,32 @@ struct __pyx_vtabstruct_10TabProxies_GTFProxy {
static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
-/* "TabProxies.pxd":72
- * pass
+/* "ctabix.pyx":771
+ * return self.__cnext__()
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
*
- * cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_BedProxy {
- struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *);
};
-static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
+static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator;
-/* "ctabix.pyx":706
- * ## Iterators for parsing through unindexed files.
- * #########################################################
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * '''iterate over ``infile``.
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *);
+struct __pyx_vtabstruct_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -1196,20 +1199,21 @@ static char __pyx_k_34[] = "could not open '%s' for reading";
static char __pyx_k_36[] = "writing failed";
static char __pyx_k_40[] = "#";
static char __pyx_k_42[] = "No such file '%s'";
-static char __pyx_k_43[] = ".gz";
-static char __pyx_k_45[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
-static char __pyx_k_47[] = "unknown preset '%s', valid presets are '%s'";
-static char __pyx_k_48[] = ",";
-static char __pyx_k_49[] = "I/O operation on closed file.";
-static char __pyx_k_52[] = "incomplete line at %s";
-static char __pyx_k_56[] = "tabix_generic_iterator";
-static char __pyx_k_57[] = "filename associated with this object.";
-static char __pyx_k_58[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n ";
-static char __pyx_k_59[] = "chromosome names";
-static char __pyx_k_60[] = "getfilesystemencoding";
-static char __pyx_k_63[] = "/ifs/devel/pysam/pysam/ctabix.pyx";
-static char __pyx_k_74[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
-static char __pyx_k_77[] = "tabix_inplace_iterator";
+static char __pyx_k_43[] = "neither preset nor seq_col,start_col and end_col given";
+static char __pyx_k_45[] = ".gz";
+static char __pyx_k_47[] = "Filename '%s.tbi' already exists, use *force* to overwrite";
+static char __pyx_k_49[] = "unknown preset '%s', valid presets are '%s'";
+static char __pyx_k_50[] = ",";
+static char __pyx_k_51[] = "I/O operation on closed file.";
+static char __pyx_k_54[] = "incomplete line at %s";
+static char __pyx_k_58[] = "tabix_generic_iterator";
+static char __pyx_k_59[] = "filename associated with this object.";
+static char __pyx_k_60[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n ";
+static char __pyx_k_61[] = "chromosome names";
+static char __pyx_k_62[] = "getfilesystemencoding";
+static char __pyx_k_65[] = "/home/andreas/devel/pysam/pysam/ctabix.pyx";
+static char __pyx_k_76[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
+static char __pyx_k_79[] = "tabix_inplace_iterator";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__r[] = "r";
@@ -1331,17 +1335,18 @@ static PyObject *__pyx_kp_s_42;
static PyObject *__pyx_kp_s_43;
static PyObject *__pyx_kp_s_45;
static PyObject *__pyx_kp_s_47;
-static PyObject *__pyx_kp_s_48;
static PyObject *__pyx_kp_s_49;
static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_52;
-static PyObject *__pyx_n_s_56;
+static PyObject *__pyx_kp_s_50;
+static PyObject *__pyx_kp_s_51;
+static PyObject *__pyx_kp_s_54;
+static PyObject *__pyx_n_s_58;
static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_n_s_60;
-static PyObject *__pyx_kp_s_63;
+static PyObject *__pyx_n_s_62;
+static PyObject *__pyx_kp_s_65;
static PyObject *__pyx_kp_s_7;
-static PyObject *__pyx_kp_s_74;
-static PyObject *__pyx_n_s_77;
+static PyObject *__pyx_kp_s_76;
+static PyObject *__pyx_n_s_79;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__IOError;
static PyObject *__pyx_n_s__KeyError;
@@ -1473,25 +1478,26 @@ static PyObject *__pyx_k_tuple_37;
static PyObject *__pyx_k_tuple_38;
static PyObject *__pyx_k_tuple_44;
static PyObject *__pyx_k_tuple_46;
-static PyObject *__pyx_k_tuple_50;
-static PyObject *__pyx_k_tuple_51;
+static PyObject *__pyx_k_tuple_48;
+static PyObject *__pyx_k_tuple_52;
static PyObject *__pyx_k_tuple_53;
-static PyObject *__pyx_k_tuple_54;
static PyObject *__pyx_k_tuple_55;
-static PyObject *__pyx_k_tuple_61;
-static PyObject *__pyx_k_tuple_64;
+static PyObject *__pyx_k_tuple_56;
+static PyObject *__pyx_k_tuple_57;
+static PyObject *__pyx_k_tuple_63;
static PyObject *__pyx_k_tuple_66;
static PyObject *__pyx_k_tuple_68;
static PyObject *__pyx_k_tuple_70;
static PyObject *__pyx_k_tuple_72;
-static PyObject *__pyx_k_tuple_75;
-static PyObject *__pyx_k_codeobj_62;
-static PyObject *__pyx_k_codeobj_65;
+static PyObject *__pyx_k_tuple_74;
+static PyObject *__pyx_k_tuple_77;
+static PyObject *__pyx_k_codeobj_64;
static PyObject *__pyx_k_codeobj_67;
static PyObject *__pyx_k_codeobj_69;
static PyObject *__pyx_k_codeobj_71;
static PyObject *__pyx_k_codeobj_73;
-static PyObject *__pyx_k_codeobj_76;
+static PyObject *__pyx_k_codeobj_75;
+static PyObject *__pyx_k_codeobj_78;
/* "ctabix.pyx":19
* from cpython.version cimport PY_MAJOR_VERSION
@@ -4319,6 +4325,7 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
+ tabix_t *__pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -4352,7 +4359,8 @@ static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_T
*
* if tid < 0:
*/
- __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
+ __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
+ __pyx_v_self->tabixfile = __pyx_t_4;
/* "ctabix.pyx":293
* self.tabixfile = tabixfile.tabixfile
@@ -4713,6 +4721,7 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
+ tabix_t *__pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -4746,7 +4755,8 @@ static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ct
*
* self.iterator = ti_query(self.tabixfile, NULL, 0, 0)
*/
- __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
+ __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
+ __pyx_v_self->tabixfile = __pyx_t_4;
/* "ctabix.pyx":344
* self.tabixfile = tabixfile.tabixfile
@@ -5576,6 +5586,7 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
+ tabix_t *__pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -5622,7 +5633,8 @@ static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ct
*
* if tid < 0:
*/
- __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
+ __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
+ __pyx_v_self->tabixfile = __pyx_t_4;
/* "ctabix.pyx":530
* self.tabixfile = tabixfile.tabixfile
@@ -6512,23 +6524,25 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
PyObject *__pyx_t_3 = NULL;
int __pyx_t_4;
int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
+ int __pyx_t_6;
int __pyx_t_7;
- PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_8;
PyObject *__pyx_t_9 = NULL;
PyObject *__pyx_t_10 = NULL;
- int __pyx_t_11;
+ PyObject *__pyx_t_11 = NULL;
PyObject *__pyx_t_12 = NULL;
- PyObject *__pyx_t_13 = NULL;
+ int __pyx_t_13;
PyObject *__pyx_t_14 = NULL;
- PyObject *(*__pyx_t_15)(PyObject *);
- int32_t __pyx_t_16;
- int32_t __pyx_t_17;
+ PyObject *__pyx_t_15 = NULL;
+ PyObject *__pyx_t_16 = NULL;
+ PyObject *(*__pyx_t_17)(PyObject *);
int32_t __pyx_t_18;
int32_t __pyx_t_19;
int32_t __pyx_t_20;
int32_t __pyx_t_21;
- char *__pyx_t_22;
+ int32_t __pyx_t_22;
+ int32_t __pyx_t_23;
+ char *__pyx_t_24;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -6542,7 +6556,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
*
* if not os.path.exists(filename): raise IOError("No such file '%s'" % filename) # <<<<<<<<<<<<<<
*
- * if not filename.endswith(".gz"):
+ * if preset == None and (seq_col == None or start_col == None or end_col == None):
*/
__pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -6585,32 +6599,84 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
/* "ctabix.pyx":655
* if not os.path.exists(filename): raise IOError("No such file '%s'" % filename)
*
- * if not filename.endswith(".gz"): # <<<<<<<<<<<<<<
- * tabix_compress( filename, filename + ".gz", force = force )
- * os.unlink( filename )
+ * if preset == None and (seq_col == None or start_col == None or end_col == None): # <<<<<<<<<<<<<<
+ * raise ValueError("neither preset nor seq_col,start_col and end_col given" )
+ *
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__endswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_44), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_preset, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = (!__pyx_t_5);
+ if (__pyx_t_5) {
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (!__pyx_t_4) {
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (!__pyx_t_6) {
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_8 = __pyx_t_7;
+ } else {
+ __pyx_t_8 = __pyx_t_6;
+ }
+ __pyx_t_6 = __pyx_t_8;
+ } else {
+ __pyx_t_6 = __pyx_t_4;
+ }
+ __pyx_t_4 = __pyx_t_6;
+ } else {
+ __pyx_t_4 = __pyx_t_5;
+ }
if (__pyx_t_4) {
/* "ctabix.pyx":656
*
+ * if preset == None and (seq_col == None or start_col == None or end_col == None):
+ * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) # <<<<<<<<<<<<<<
+ *
+ * if not filename.endswith(".gz"):
+ */
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_44), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
+
+ /* "ctabix.pyx":658
+ * raise ValueError("neither preset nor seq_col,start_col and end_col given" )
+ *
+ * if not filename.endswith(".gz"): # <<<<<<<<<<<<<<
+ * tabix_compress( filename, filename + ".gz", force = force )
+ * os.unlink( filename )
+ */
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__endswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_46), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = (!__pyx_t_4);
+ if (__pyx_t_5) {
+
+ /* "ctabix.pyx":659
+ *
* if not filename.endswith(".gz"):
* tabix_compress( filename, filename + ".gz", force = force ) # <<<<<<<<<<<<<<
* os.unlink( filename )
* filename += ".gz"
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__tabix_compress); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__tabix_compress); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_43)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_45)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename);
@@ -6618,126 +6684,126 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_3));
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__force), __pyx_v_force) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__force), __pyx_v_force) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "ctabix.pyx":657
+ /* "ctabix.pyx":660
* if not filename.endswith(".gz"):
* tabix_compress( filename, filename + ".gz", force = force )
* os.unlink( filename ) # <<<<<<<<<<<<<<
* filename += ".gz"
*
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__unlink); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__unlink); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "ctabix.pyx":658
+ /* "ctabix.pyx":661
* tabix_compress( filename, filename + ".gz", force = force )
* os.unlink( filename )
* filename += ".gz" # <<<<<<<<<<<<<<
*
* if not force and os.path.exists(filename + ".tbi" ):
*/
- __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_filename, ((PyObject *)__pyx_kp_s_43)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_filename, ((PyObject *)__pyx_kp_s_45)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_filename);
__pyx_v_filename = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L4;
+ goto __pyx_L5;
}
- __pyx_L4:;
+ __pyx_L5:;
- /* "ctabix.pyx":660
+ /* "ctabix.pyx":663
* filename += ".gz"
*
* if not force and os.path.exists(filename + ".tbi" ): # <<<<<<<<<<<<<<
* raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" )
*
*/
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_force); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = (!__pyx_t_4);
- if (__pyx_t_5) {
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_force); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (!__pyx_t_5);
+ if (__pyx_t_4) {
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_7 = __pyx_t_4;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_6 = __pyx_t_5;
} else {
- __pyx_t_7 = __pyx_t_5;
+ __pyx_t_6 = __pyx_t_4;
}
- if (__pyx_t_7) {
+ if (__pyx_t_6) {
- /* "ctabix.pyx":661
+ /* "ctabix.pyx":664
*
* if not force and os.path.exists(filename + ".tbi" ):
* raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" ) # <<<<<<<<<<<<<<
*
* # columns (1-based)
*/
- __pyx_t_6 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_k_tuple_46), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_Raise(__pyx_t_6, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_k_tuple_48), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_Raise(__pyx_t_9, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L6;
}
- __pyx_L5:;
+ __pyx_L6:;
- /* "ctabix.pyx":666
+ /* "ctabix.pyx":669
* # preset-code, contig, start, end, metachar for commends, lines to ignore at beginning
* # 0 is a missing column
* preset2conf = { # <<<<<<<<<<<<<<
* 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ),
* 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ),
*/
- __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
- /* "ctabix.pyx":667
+ /* "ctabix.pyx":670
* # 0 is a missing column
* preset2conf = {
* 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), # <<<<<<<<<<<<<<
* 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ),
* 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ),
*/
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_0);
@@ -6757,17 +6823,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__gff), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__gff), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "ctabix.pyx":668
+ /* "ctabix.pyx":671
* preset2conf = {
* 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ),
* 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), # <<<<<<<<<<<<<<
* 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ),
* 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ),
*/
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_int_65536);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_65536);
@@ -6787,17 +6853,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__bed), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__bed), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "ctabix.pyx":669
+ /* "ctabix.pyx":672
* 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ),
* 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ),
* 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), # <<<<<<<<<<<<<<
* 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ),
* 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ),
*/
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_int_65536);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_65536);
@@ -6817,17 +6883,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__psltbl), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__psltbl), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "ctabix.pyx":670
+ /* "ctabix.pyx":673
* 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ),
* 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ),
* 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ), # <<<<<<<<<<<<<<
* 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ),
* 'pileup': (3, 1, 2, 0, ord('#'), 0 ),
*/
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_int_1);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_1);
@@ -6847,17 +6913,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__sam), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__sam), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "ctabix.pyx":671
+ /* "ctabix.pyx":674
* 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ),
* 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ),
* 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ), # <<<<<<<<<<<<<<
* 'pileup': (3, 1, 2, 0, ord('#'), 0 ),
* }
*/
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_int_2);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_2);
@@ -6877,17 +6943,17 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__vcf), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__vcf), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "ctabix.pyx":672
+ /* "ctabix.pyx":675
* 'sam' : ( 1, 3, 4, 0, ord('#'), 0 ),
* 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ),
* 'pileup': (3, 1, 2, 0, ord('#'), 0 ), # <<<<<<<<<<<<<<
* }
*
*/
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_int_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_int_3);
@@ -6907,22 +6973,22 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 5, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__pileup), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__pileup), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_v_preset2conf = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_preset2conf = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "ctabix.pyx":675
+ /* "ctabix.pyx":678
* }
*
* if preset: # <<<<<<<<<<<<<<
* try:
* conf_data = preset2conf[preset]
*/
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_preset); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_7) {
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_preset); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_6) {
- /* "ctabix.pyx":676
+ /* "ctabix.pyx":679
*
* if preset:
* try: # <<<<<<<<<<<<<<
@@ -6930,132 +6996,132 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
* except KeyError:
*/
{
- __Pyx_ExceptionSave(&__pyx_t_8, &__pyx_t_9, &__pyx_t_10);
- __Pyx_XGOTREF(__pyx_t_8);
- __Pyx_XGOTREF(__pyx_t_9);
+ __Pyx_ExceptionSave(&__pyx_t_10, &__pyx_t_11, &__pyx_t_12);
__Pyx_XGOTREF(__pyx_t_10);
+ __Pyx_XGOTREF(__pyx_t_11);
+ __Pyx_XGOTREF(__pyx_t_12);
/*try:*/ {
- /* "ctabix.pyx":677
+ /* "ctabix.pyx":680
* if preset:
* try:
* conf_data = preset2conf[preset] # <<<<<<<<<<<<<<
* except KeyError:
* raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys() )))
*/
- __pyx_t_6 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_preset2conf), __pyx_v_preset); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_v_conf_data = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_t_9 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_preset2conf), __pyx_v_preset); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_v_conf_data = __pyx_t_9;
+ __pyx_t_9 = 0;
}
- __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L14_try_end;
- __pyx_L7_error:;
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
+ goto __pyx_L15_try_end;
+ __pyx_L8_error:;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "ctabix.pyx":678
+ /* "ctabix.pyx":681
* try:
* conf_data = preset2conf[preset]
* except KeyError: # <<<<<<<<<<<<<<
* raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys() )))
* else:
*/
- __pyx_t_11 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
- if (__pyx_t_11) {
+ __pyx_t_13 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
+ if (__pyx_t_13) {
__Pyx_AddTraceback("ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_3, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_3, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_GOTREF(__pyx_t_3);
__Pyx_GOTREF(__pyx_t_1);
- /* "ctabix.pyx":679
+ /* "ctabix.pyx":682
* conf_data = preset2conf[preset]
* except KeyError:
* raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys() ))) # <<<<<<<<<<<<<<
* else:
* if end_col == None: end_col = -1
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_48), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_50), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_12 = PyDict_Keys(__pyx_v_preset2conf); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_13);
- PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_12);
- __Pyx_GIVEREF(__pyx_t_12);
- __pyx_t_12 = 0;
- __pyx_t_12 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __pyx_t_14 = PyDict_Keys(__pyx_v_preset2conf); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(__pyx_t_14);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(2); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
+ __pyx_t_15 = PyTuple_New(2); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(__pyx_v_preset);
- PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_v_preset);
+ PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_preset);
__Pyx_GIVEREF(__pyx_v_preset);
- PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_12);
- __Pyx_GIVEREF(__pyx_t_12);
- __pyx_t_12 = 0;
- __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_47), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_12));
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_13);
- PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_12));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_12));
- __pyx_t_12 = 0;
- __pyx_t_12 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(__pyx_t_12);
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __Pyx_Raise(__pyx_t_12, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ PyTuple_SET_ITEM(__pyx_t_15, 1, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_49), ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
+ __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
+ __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_t_14));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_14));
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
+ __Pyx_Raise(__pyx_t_14, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L8_exception_handled;
+ goto __pyx_L9_exception_handled;
}
- __pyx_L9_except_error:;
- __Pyx_XGIVEREF(__pyx_t_8);
- __Pyx_XGIVEREF(__pyx_t_9);
+ __pyx_L10_except_error:;
__Pyx_XGIVEREF(__pyx_t_10);
- __Pyx_ExceptionReset(__pyx_t_8, __pyx_t_9, __pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_XGIVEREF(__pyx_t_12);
+ __Pyx_ExceptionReset(__pyx_t_10, __pyx_t_11, __pyx_t_12);
goto __pyx_L1_error;
- __pyx_L8_exception_handled:;
- __Pyx_XGIVEREF(__pyx_t_8);
- __Pyx_XGIVEREF(__pyx_t_9);
+ __pyx_L9_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_10);
- __Pyx_ExceptionReset(__pyx_t_8, __pyx_t_9, __pyx_t_10);
- __pyx_L14_try_end:;
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_XGIVEREF(__pyx_t_12);
+ __Pyx_ExceptionReset(__pyx_t_10, __pyx_t_11, __pyx_t_12);
+ __pyx_L15_try_end:;
}
- goto __pyx_L6;
+ goto __pyx_L7;
}
/*else*/ {
- /* "ctabix.pyx":681
+ /* "ctabix.pyx":684
* raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys() )))
* else:
* if end_col == None: end_col = -1 # <<<<<<<<<<<<<<
* preset = 0
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_7) {
+ if (__pyx_t_6) {
__Pyx_INCREF(__pyx_int_neg_1);
__Pyx_DECREF(__pyx_v_end_col);
__pyx_v_end_col = __pyx_int_neg_1;
- goto __pyx_L17;
+ goto __pyx_L18;
}
- __pyx_L17:;
+ __pyx_L18:;
- /* "ctabix.pyx":682
+ /* "ctabix.pyx":685
* else:
* if end_col == None: end_col = -1
* preset = 0 # <<<<<<<<<<<<<<
@@ -7066,71 +7132,71 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_DECREF(__pyx_v_preset);
__pyx_v_preset = __pyx_int_0;
- /* "ctabix.pyx":689
+ /* "ctabix.pyx":692
* # -1 is subtracted from the start coordinate. To avoid doing this, set
* # the TI_FLAG_UCSC=0x10000 flag:
* if zerobased: preset = preset | 0x10000 # <<<<<<<<<<<<<<
*
* conf_data = (preset, seq_col+1, start_col+1, end_col+1, ord(meta_char), 0)
*/
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_zerobased); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_7) {
- __pyx_t_1 = PyNumber_Or(__pyx_v_preset, __pyx_int_65536); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_v_zerobased); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_6) {
+ __pyx_t_1 = PyNumber_Or(__pyx_v_preset, __pyx_int_65536); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_preset);
__pyx_v_preset = __pyx_t_1;
__pyx_t_1 = 0;
- goto __pyx_L18;
+ goto __pyx_L19;
}
- __pyx_L18:;
+ __pyx_L19:;
- /* "ctabix.pyx":691
+ /* "ctabix.pyx":694
* if zerobased: preset = preset | 0x10000
*
* conf_data = (preset, seq_col+1, start_col+1, end_col+1, ord(meta_char), 0) # <<<<<<<<<<<<<<
*
* cdef ti_conf_t conf
*/
- __pyx_t_1 = PyNumber_Add(__pyx_v_seq_col, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_v_seq_col, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyNumber_Add(__pyx_v_start_col, __pyx_int_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(__pyx_v_start_col, __pyx_int_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyNumber_Add(__pyx_v_end_col, __pyx_int_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_12 = PyTuple_New(1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __pyx_t_9 = PyNumber_Add(__pyx_v_end_col, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
__Pyx_INCREF(__pyx_v_meta_char);
- PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_v_meta_char);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_meta_char);
__Pyx_GIVEREF(__pyx_v_meta_char);
- __pyx_t_13 = PyObject_Call(__pyx_builtin_ord, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
- __pyx_t_12 = PyTuple_New(6); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __pyx_t_15 = PyObject_Call(__pyx_builtin_ord, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __pyx_t_14 = PyTuple_New(6); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
__Pyx_INCREF(__pyx_v_preset);
- PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_v_preset);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_preset);
__Pyx_GIVEREF(__pyx_v_preset);
- PyTuple_SET_ITEM(__pyx_t_12, 1, __pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_12, 2, __pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_14, 2, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_12, 3, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_12, 4, __pyx_t_13);
- __Pyx_GIVEREF(__pyx_t_13);
+ PyTuple_SET_ITEM(__pyx_t_14, 3, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_14, 4, __pyx_t_15);
+ __Pyx_GIVEREF(__pyx_t_15);
__Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_12, 5, __pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_t_14, 5, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
__pyx_t_1 = 0;
__pyx_t_3 = 0;
- __pyx_t_6 = 0;
- __pyx_t_13 = 0;
- __pyx_v_conf_data = ((PyObject *)__pyx_t_12);
- __pyx_t_12 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_15 = 0;
+ __pyx_v_conf_data = ((PyObject *)__pyx_t_14);
+ __pyx_t_14 = 0;
}
- __pyx_L6:;
+ __pyx_L7:;
- /* "ctabix.pyx":694
+ /* "ctabix.pyx":697
*
* cdef ti_conf_t conf
* conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data # <<<<<<<<<<<<<<
@@ -7147,103 +7213,103 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
if (unlikely(size != 6)) {
if (size > 6) __Pyx_RaiseTooManyValuesError(6);
else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__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))) {
- __pyx_t_12 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_13 = PyTuple_GET_ITEM(sequence, 1);
- __pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
+ __pyx_t_14 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_15 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 3);
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 4);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 5);
} else {
- __pyx_t_12 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_13 = PyList_GET_ITEM(sequence, 1);
- __pyx_t_6 = PyList_GET_ITEM(sequence, 2);
+ __pyx_t_14 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_15 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 2);
__pyx_t_3 = PyList_GET_ITEM(sequence, 3);
__pyx_t_1 = PyList_GET_ITEM(sequence, 4);
__pyx_t_2 = PyList_GET_ITEM(sequence, 5);
}
- __Pyx_INCREF(__pyx_t_12);
- __Pyx_INCREF(__pyx_t_13);
- __Pyx_INCREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_14);
+ __Pyx_INCREF(__pyx_t_15);
+ __Pyx_INCREF(__pyx_t_9);
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_2);
#else
Py_ssize_t i;
- PyObject** temps[6] = {&__pyx_t_12,&__pyx_t_13,&__pyx_t_6,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2};
+ PyObject** temps[6] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_9,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2};
for (i=0; i < 6; i++) {
- PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
*(temps[i]) = item;
}
#endif
} else
{
Py_ssize_t index = -1;
- PyObject** temps[6] = {&__pyx_t_12,&__pyx_t_13,&__pyx_t_6,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2};
- __pyx_t_14 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_15 = Py_TYPE(__pyx_t_14)->tp_iternext;
+ PyObject** temps[6] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_9,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2};
+ __pyx_t_16 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_16);
+ __pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext;
for (index=0; index < 6; index++) {
- PyObject* item = __pyx_t_15(__pyx_t_14); if (unlikely(!item)) goto __pyx_L19_unpacking_failed;
+ PyObject* item = __pyx_t_17(__pyx_t_16); if (unlikely(!item)) goto __pyx_L20_unpacking_failed;
__Pyx_GOTREF(item);
*(temps[index]) = item;
}
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_15(__pyx_t_14), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_15 = NULL;
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- goto __pyx_L20_unpacking_done;
- __pyx_L19_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_t_15 = NULL;
+ 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);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L20_unpacking_done:;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L21_unpacking_done:;
}
- __pyx_t_16 = __Pyx_PyInt_from_py_int32_t(__pyx_t_12); if (unlikely((__pyx_t_16 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_t_17 = __Pyx_PyInt_from_py_int32_t(__pyx_t_13); if (unlikely((__pyx_t_17 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_18 = __Pyx_PyInt_from_py_int32_t(__pyx_t_6); if (unlikely((__pyx_t_18 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_19 = __Pyx_PyInt_from_py_int32_t(__pyx_t_3); if (unlikely((__pyx_t_19 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = __Pyx_PyInt_from_py_int32_t(__pyx_t_14); if (unlikely((__pyx_t_18 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_19 = __Pyx_PyInt_from_py_int32_t(__pyx_t_15); if (unlikely((__pyx_t_19 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ __pyx_t_20 = __Pyx_PyInt_from_py_int32_t(__pyx_t_9); if (unlikely((__pyx_t_20 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_21 = __Pyx_PyInt_from_py_int32_t(__pyx_t_3); if (unlikely((__pyx_t_21 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_20 = __Pyx_PyInt_from_py_int32_t(__pyx_t_1); if (unlikely((__pyx_t_20 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_PyInt_from_py_int32_t(__pyx_t_1); if (unlikely((__pyx_t_22 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_21 = __Pyx_PyInt_from_py_int32_t(__pyx_t_2); if (unlikely((__pyx_t_21 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_23 = __Pyx_PyInt_from_py_int32_t(__pyx_t_2); if (unlikely((__pyx_t_23 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_conf.preset = __pyx_t_16;
- __pyx_v_conf.sc = __pyx_t_17;
- __pyx_v_conf.bc = __pyx_t_18;
- __pyx_v_conf.ec = __pyx_t_19;
- __pyx_v_conf.meta_char = __pyx_t_20;
- __pyx_v_conf.line_skip = __pyx_t_21;
-
- /* "ctabix.pyx":696
+ __pyx_v_conf.preset = __pyx_t_18;
+ __pyx_v_conf.sc = __pyx_t_19;
+ __pyx_v_conf.bc = __pyx_t_20;
+ __pyx_v_conf.ec = __pyx_t_21;
+ __pyx_v_conf.meta_char = __pyx_t_22;
+ __pyx_v_conf.line_skip = __pyx_t_23;
+
+ /* "ctabix.pyx":699
* conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data
*
* fn = _my_encodeFilename( filename ) # <<<<<<<<<<<<<<
* ti_index_build( fn, &conf)
*
*/
- __pyx_t_2 = ((PyObject *)__pyx_f_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__pyx_f_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_fn = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "ctabix.pyx":697
+ /* "ctabix.pyx":700
*
* fn = _my_encodeFilename( filename )
* ti_index_build( fn, &conf) # <<<<<<<<<<<<<<
*
* return filename
*/
- __pyx_t_22 = PyBytes_AsString(((PyObject *)__pyx_v_fn)); if (unlikely((!__pyx_t_22) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ti_index_build(__pyx_t_22, (&__pyx_v_conf));
+ __pyx_t_24 = PyBytes_AsString(((PyObject *)__pyx_v_fn)); if (unlikely((!__pyx_t_24) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ ti_index_build(__pyx_t_24, (&__pyx_v_conf));
- /* "ctabix.pyx":699
+ /* "ctabix.pyx":702
* ti_index_build( fn, &conf)
*
* return filename # <<<<<<<<<<<<<<
@@ -7261,10 +7327,10 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_12);
- __Pyx_XDECREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_14);
+ __Pyx_XDECREF(__pyx_t_15);
+ __Pyx_XDECREF(__pyx_t_16);
__Pyx_AddTraceback("ctabix.tabix_index", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
@@ -7311,7 +7377,7 @@ static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ 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;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -7323,14 +7389,14 @@ static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_
}
__pyx_v_infile = values[0];
if (values[1]) {
- __pyx_v_buffer_size = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_buffer_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_buffer_size = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_buffer_size == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_buffer_size = ((int)65536);
}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ctabix.tabix_inplace_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -7341,7 +7407,7 @@ static int __pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_
return __pyx_r;
}
-/* "ctabix.pyx":716
+/* "ctabix.pyx":719
*
*
* def __cinit__(self, infile, int buffer_size = 65536 ): # <<<<<<<<<<<<<<
@@ -7361,17 +7427,17 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__cinit__", 0);
- /* "ctabix.pyx":718
+ /* "ctabix.pyx":721
* def __cinit__(self, infile, int buffer_size = 65536 ):
*
* cdef int fd = PyObject_AsFileDescriptor( infile ) # <<<<<<<<<<<<<<
* if fd == -1: raise ValueError( "I/O operation on closed file." )
* self.infile = fdopen( fd, 'r')
*/
- __pyx_t_1 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 721; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_fd = __pyx_t_1;
- /* "ctabix.pyx":719
+ /* "ctabix.pyx":722
*
* cdef int fd = PyObject_AsFileDescriptor( infile )
* if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
@@ -7380,16 +7446,16 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_
*/
__pyx_t_2 = (__pyx_v_fd == -1);
if (__pyx_t_2) {
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_50), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_52), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L3;
}
__pyx_L3:;
- /* "ctabix.pyx":720
+ /* "ctabix.pyx":723
* cdef int fd = PyObject_AsFileDescriptor( infile )
* if fd == -1: raise ValueError( "I/O operation on closed file." )
* self.infile = fdopen( fd, 'r') # <<<<<<<<<<<<<<
@@ -7398,7 +7464,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_
*/
__pyx_v_self->infile = fdopen(__pyx_v_fd, __pyx_k__r);
- /* "ctabix.pyx":722
+ /* "ctabix.pyx":725
* self.infile = fdopen( fd, 'r')
*
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
@@ -7407,16 +7473,16 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_
*/
__pyx_t_2 = (__pyx_v_self->infile == NULL);
if (__pyx_t_2) {
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_51), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_53), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L4;
}
__pyx_L4:;
- /* "ctabix.pyx":724
+ /* "ctabix.pyx":727
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
*
* self.buffer = <char*>malloc( buffer_size ) # <<<<<<<<<<<<<<
@@ -7425,7 +7491,7 @@ static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_
*/
__pyx_v_self->buffer = ((char *)malloc(__pyx_v_buffer_size));
- /* "ctabix.pyx":725
+ /* "ctabix.pyx":728
*
* self.buffer = <char*>malloc( buffer_size )
* self.size = buffer_size # <<<<<<<<<<<<<<
@@ -7456,7 +7522,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_3__iter__(PyObject *_
return __pyx_r;
}
-/* "ctabix.pyx":727
+/* "ctabix.pyx":730
* self.size = buffer_size
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -7469,7 +7535,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __py
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__iter__", 0);
- /* "ctabix.pyx":728
+ /* "ctabix.pyx":731
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -7488,7 +7554,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __py
return __pyx_r;
}
-/* "ctabix.pyx":730
+/* "ctabix.pyx":733
* return self
*
* cdef __cnext__(self): # <<<<<<<<<<<<<<
@@ -7503,44 +7569,46 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx
char *__pyx_v_result;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
+ char *__pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_t_4;
int __pyx_t_5;
int __pyx_t_6;
- PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_7;
PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__cnext__", 0);
- /* "ctabix.pyx":734
+ /* "ctabix.pyx":737
* cdef char * b
* cdef size_t nbytes
* b = self.buffer # <<<<<<<<<<<<<<
* r = self.Parser()
*
*/
- __pyx_v_b = __pyx_v_self->buffer;
+ __pyx_t_1 = __pyx_v_self->buffer;
+ __pyx_v_b = __pyx_t_1;
- /* "ctabix.pyx":735
+ /* "ctabix.pyx":738
* cdef size_t nbytes
* b = self.buffer
* r = self.Parser() # <<<<<<<<<<<<<<
*
* while not feof( self.infile ):
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_v_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_r = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "ctabix.pyx":737
+ /* "ctabix.pyx":740
* r = self.Parser()
*
* while not feof( self.infile ): # <<<<<<<<<<<<<<
@@ -7548,10 +7616,10 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx
*
*/
while (1) {
- __pyx_t_3 = (!feof(__pyx_v_self->infile));
- if (!__pyx_t_3) break;
+ __pyx_t_4 = (!feof(__pyx_v_self->infile));
+ if (!__pyx_t_4) break;
- /* "ctabix.pyx":738
+ /* "ctabix.pyx":741
*
* while not feof( self.infile ):
* nbytes = getline( &b, &self.size, self.infile) # <<<<<<<<<<<<<<
@@ -7560,77 +7628,77 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx
*/
__pyx_v_nbytes = getline((&__pyx_v_b), (&__pyx_v_self->size), __pyx_v_self->infile);
- /* "ctabix.pyx":741
+ /* "ctabix.pyx":744
*
* # stop at first error or eof
* if (nbytes == -1): break # <<<<<<<<<<<<<<
* # skip comments
* if (b[0] == '#'): continue
*/
- __pyx_t_3 = (__pyx_v_nbytes == -1);
- if (__pyx_t_3) {
+ __pyx_t_4 = (__pyx_v_nbytes == -1);
+ if (__pyx_t_4) {
goto __pyx_L4_break;
goto __pyx_L5;
}
__pyx_L5:;
- /* "ctabix.pyx":743
+ /* "ctabix.pyx":746
* if (nbytes == -1): break
* # skip comments
* if (b[0] == '#'): continue # <<<<<<<<<<<<<<
*
* # skip empty lines
*/
- __pyx_t_3 = ((__pyx_v_b[0]) == '#');
- if (__pyx_t_3) {
+ __pyx_t_4 = ((__pyx_v_b[0]) == '#');
+ if (__pyx_t_4) {
goto __pyx_L3_continue;
goto __pyx_L6;
}
__pyx_L6:;
- /* "ctabix.pyx":746
+ /* "ctabix.pyx":749
*
* # skip empty lines
* if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # <<<<<<<<<<<<<<
*
* # make sure that entry is complete
*/
- __pyx_t_3 = ((__pyx_v_b[0]) == '\x00');
- if (!__pyx_t_3) {
- __pyx_t_4 = ((__pyx_v_b[0]) == '\n');
- if (!__pyx_t_4) {
- __pyx_t_5 = ((__pyx_v_b[0]) == '\r');
- __pyx_t_6 = __pyx_t_5;
+ __pyx_t_4 = ((__pyx_v_b[0]) == '\x00');
+ if (!__pyx_t_4) {
+ __pyx_t_5 = ((__pyx_v_b[0]) == '\n');
+ if (!__pyx_t_5) {
+ __pyx_t_6 = ((__pyx_v_b[0]) == '\r');
+ __pyx_t_7 = __pyx_t_6;
} else {
- __pyx_t_6 = __pyx_t_4;
+ __pyx_t_7 = __pyx_t_5;
}
- __pyx_t_4 = __pyx_t_6;
+ __pyx_t_5 = __pyx_t_7;
} else {
- __pyx_t_4 = __pyx_t_3;
+ __pyx_t_5 = __pyx_t_4;
}
- if (__pyx_t_4) {
+ if (__pyx_t_5) {
goto __pyx_L3_continue;
goto __pyx_L7;
}
__pyx_L7:;
- /* "ctabix.pyx":749
+ /* "ctabix.pyx":752
*
* # make sure that entry is complete
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # <<<<<<<<<<<<<<
* result = b
* raise ValueError( "incomplete line at %s" % result )
*/
- __pyx_t_4 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n');
- if (__pyx_t_4) {
- __pyx_t_3 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r');
- __pyx_t_6 = __pyx_t_3;
+ __pyx_t_5 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n');
+ if (__pyx_t_5) {
+ __pyx_t_4 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r');
+ __pyx_t_7 = __pyx_t_4;
} else {
- __pyx_t_6 = __pyx_t_4;
+ __pyx_t_7 = __pyx_t_5;
}
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
- /* "ctabix.pyx":750
+ /* "ctabix.pyx":753
* # make sure that entry is complete
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
* result = b # <<<<<<<<<<<<<<
@@ -7639,61 +7707,61 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx
*/
__pyx_v_result = __pyx_v_b;
- /* "ctabix.pyx":751
+ /* "ctabix.pyx":754
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
* result = b
* raise ValueError( "incomplete line at %s" % result ) # <<<<<<<<<<<<<<
*
* # make sure that this goes fully through C
*/
- __pyx_t_2 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_52), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
}
__pyx_L8:;
- /* "ctabix.pyx":757
+ /* "ctabix.pyx":760
* # Python object causing segfaults as
* # the wrong memory is freed
* r.present( b, nbytes ) # <<<<<<<<<<<<<<
* return r
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__present); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_7 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__present); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_8 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_2 = 0;
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_3 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "ctabix.pyx":758
+ /* "ctabix.pyx":761
* # the wrong memory is freed
* r.present( b, nbytes )
* return r # <<<<<<<<<<<<<<
@@ -7708,7 +7776,7 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx
}
__pyx_L4_break:;
- /* "ctabix.pyx":760
+ /* "ctabix.pyx":763
* return r
*
* raise StopIteration # <<<<<<<<<<<<<<
@@ -7716,15 +7784,15 @@ static PyObject *__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__(struct __pyx
* def __dealloc__(self):
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
__Pyx_AddTraceback("ctabix.tabix_inplace_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
@@ -7743,7 +7811,7 @@ static void __pyx_pw_6ctabix_22tabix_inplace_iterator_5__dealloc__(PyObject *__p
__Pyx_RefNannyFinishContext();
}
-/* "ctabix.pyx":762
+/* "ctabix.pyx":765
* raise StopIteration
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -7755,7 +7823,7 @@ static void __pyx_pf_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
- /* "ctabix.pyx":763
+ /* "ctabix.pyx":766
*
* def __dealloc__(self):
* free(self.buffer) # <<<<<<<<<<<<<<
@@ -7778,7 +7846,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__(PyObject *_
return __pyx_r;
}
-/* "ctabix.pyx":765
+/* "ctabix.pyx":768
* free(self.buffer)
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -7795,7 +7863,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __py
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__next__", 0);
- /* "ctabix.pyx":766
+ /* "ctabix.pyx":769
*
* def __next__(self):
* return self.__cnext__() # <<<<<<<<<<<<<<
@@ -7803,7 +7871,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __py
* ctypedef class tabix_copy_iterator:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -7849,11 +7917,11 @@ static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_s
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
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 = 777; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -7866,13 +7934,13 @@ static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_s
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ctabix.tabix_copy_iterator.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_6ctabix_Parser, 1, "parser", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_parser), __pyx_ptype_6ctabix_Parser, 1, "parser", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(((struct __pyx_obj_6ctabix_tabix_copy_iterator *)__pyx_v_self), __pyx_v_infile, __pyx_v_parser);
goto __pyx_L0;
__pyx_L1_error:;
@@ -7882,7 +7950,7 @@ static int __pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "ctabix.pyx":777
+/* "ctabix.pyx":780
* '''
*
* def __cinit__(self, infile, Parser parser ): # <<<<<<<<<<<<<<
@@ -7902,17 +7970,17 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__cinit__", 0);
- /* "ctabix.pyx":779
+ /* "ctabix.pyx":782
* def __cinit__(self, infile, Parser parser ):
*
* cdef int fd = PyObject_AsFileDescriptor( infile ) # <<<<<<<<<<<<<<
* if fd == -1: raise ValueError( "I/O operation on closed file." )
* self.infile = fdopen( fd, 'r')
*/
- __pyx_t_1 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_AsFileDescriptor(__pyx_v_infile); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_fd = __pyx_t_1;
- /* "ctabix.pyx":780
+ /* "ctabix.pyx":783
*
* cdef int fd = PyObject_AsFileDescriptor( infile )
* if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
@@ -7921,16 +7989,16 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct
*/
__pyx_t_2 = (__pyx_v_fd == -1);
if (__pyx_t_2) {
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_53), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_55), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L3;
}
__pyx_L3:;
- /* "ctabix.pyx":781
+ /* "ctabix.pyx":784
* cdef int fd = PyObject_AsFileDescriptor( infile )
* if fd == -1: raise ValueError( "I/O operation on closed file." )
* self.infile = fdopen( fd, 'r') # <<<<<<<<<<<<<<
@@ -7939,7 +8007,7 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct
*/
__pyx_v_self->infile = fdopen(__pyx_v_fd, __pyx_k__r);
- /* "ctabix.pyx":782
+ /* "ctabix.pyx":785
* if fd == -1: raise ValueError( "I/O operation on closed file." )
* self.infile = fdopen( fd, 'r')
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
@@ -7948,16 +8016,16 @@ static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ct
*/
__pyx_t_2 = (__pyx_v_self->infile == NULL);
if (__pyx_t_2) {
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_54), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_56), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L4;
}
__pyx_L4:;
- /* "ctabix.pyx":783
+ /* "ctabix.pyx":786
* self.infile = fdopen( fd, 'r')
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
* self.parser = parser # <<<<<<<<<<<<<<
@@ -7992,7 +8060,7 @@ static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_3__iter__(PyObject *__py
return __pyx_r;
}
-/* "ctabix.pyx":785
+/* "ctabix.pyx":788
* self.parser = parser
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -8005,7 +8073,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_o
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__iter__", 0);
- /* "ctabix.pyx":786
+ /* "ctabix.pyx":789
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -8024,7 +8092,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_o
return __pyx_r;
}
-/* "ctabix.pyx":788
+/* "ctabix.pyx":791
* return self
*
* cdef __cnext__(self): # <<<<<<<<<<<<<<
@@ -8050,7 +8118,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__cnext__", 0);
- /* "ctabix.pyx":794
+ /* "ctabix.pyx":797
* cdef int x
*
* b = NULL # <<<<<<<<<<<<<<
@@ -8059,7 +8127,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
*/
__pyx_v_b = NULL;
- /* "ctabix.pyx":796
+ /* "ctabix.pyx":799
* b = NULL
*
* while not feof( self.infile ): # <<<<<<<<<<<<<<
@@ -8070,7 +8138,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
__pyx_t_1 = (!feof(__pyx_v_self->infile));
if (!__pyx_t_1) break;
- /* "ctabix.pyx":800
+ /* "ctabix.pyx":803
* # getline allocates on demand
* # return number of characters read excluding null byte
* nbytes = getline( &b, &nbytes, self.infile) # <<<<<<<<<<<<<<
@@ -8079,7 +8147,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
*/
__pyx_v_nbytes = getline((&__pyx_v_b), (&__pyx_v_nbytes), __pyx_v_self->infile);
- /* "ctabix.pyx":802
+ /* "ctabix.pyx":805
* nbytes = getline( &b, &nbytes, self.infile)
* # stop at first error
* if (nbytes == -1): break # <<<<<<<<<<<<<<
@@ -8093,7 +8161,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
}
__pyx_L5:;
- /* "ctabix.pyx":804
+ /* "ctabix.pyx":807
* if (nbytes == -1): break
* # skip comments
* if (b[0] == '#'): continue # <<<<<<<<<<<<<<
@@ -8107,7 +8175,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
}
__pyx_L6:;
- /* "ctabix.pyx":807
+ /* "ctabix.pyx":810
*
* # skip empty lines
* if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # <<<<<<<<<<<<<<
@@ -8133,7 +8201,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
}
__pyx_L7:;
- /* "ctabix.pyx":810
+ /* "ctabix.pyx":813
*
* # make sure that entry is complete
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # <<<<<<<<<<<<<<
@@ -8149,7 +8217,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
}
if (__pyx_t_4) {
- /* "ctabix.pyx":811
+ /* "ctabix.pyx":814
* # make sure that entry is complete
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
* result = b # <<<<<<<<<<<<<<
@@ -8158,7 +8226,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
*/
__pyx_v_result = __pyx_v_b;
- /* "ctabix.pyx":812
+ /* "ctabix.pyx":815
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
* result = b
* free(b) # <<<<<<<<<<<<<<
@@ -8167,34 +8235,34 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
*/
free(__pyx_v_b);
- /* "ctabix.pyx":813
+ /* "ctabix.pyx":816
* result = b
* free(b)
* raise ValueError( "incomplete line at %s" % result ) # <<<<<<<<<<<<<<
*
* # make sure that this goes fully through C
*/
- __pyx_t_5 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_52), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
}
__pyx_L8:;
- /* "ctabix.pyx":820
+ /* "ctabix.pyx":823
* # the wrong memory is freed
* # -1 to remove the new-line character
* return self.parser(b, nbytes) # <<<<<<<<<<<<<<
@@ -8202,11 +8270,11 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
* free(b)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
@@ -8214,7 +8282,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_6 = 0;
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(((PyObject *)__pyx_v_self->parser), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(((PyObject *)__pyx_v_self->parser), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_r = __pyx_t_5;
@@ -8224,7 +8292,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
}
__pyx_L4_break:;
- /* "ctabix.pyx":822
+ /* "ctabix.pyx":825
* return self.parser(b, nbytes)
*
* free(b) # <<<<<<<<<<<<<<
@@ -8233,7 +8301,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
*/
free(__pyx_v_b);
- /* "ctabix.pyx":823
+ /* "ctabix.pyx":826
*
* free(b)
* raise StopIteration # <<<<<<<<<<<<<<
@@ -8241,7 +8309,7 @@ static PyObject *__pyx_f_6ctabix_19tabix_copy_iterator___cnext__(struct __pyx_ob
* def __next__(self):
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -8268,7 +8336,7 @@ static PyObject *__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__(PyObject *__py
return __pyx_r;
}
-/* "ctabix.pyx":825
+/* "ctabix.pyx":828
* raise StopIteration
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -8285,7 +8353,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__next__", 0);
- /* "ctabix.pyx":826
+ /* "ctabix.pyx":829
*
* def __next__(self):
* return self.__cnext__() # <<<<<<<<<<<<<<
@@ -8293,7 +8361,7 @@ static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_o
* class tabix_generic_iterator:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *)__pyx_v_self->__pyx_vtab)->__pyx___cnext__(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -8343,16 +8411,16 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *_
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -8367,7 +8435,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *_
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ctabix.tabix_generic_iterator.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -8378,7 +8446,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_1__init__(PyObject *_
return __pyx_r;
}
-/* "ctabix.pyx":833
+/* "ctabix.pyx":836
* Permits the use of file-like objects for example from the gzip module.
* '''
* def __init__(self, infile, parser ): # <<<<<<<<<<<<<<
@@ -8397,47 +8465,47 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSE
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__init__", 0);
- /* "ctabix.pyx":835
+ /* "ctabix.pyx":838
* def __init__(self, infile, parser ):
*
* self.infile = infile # <<<<<<<<<<<<<<
* if self.infile.closed: raise ValueError( "I/O operation on closed file." )
* self.parser = parser
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__infile, __pyx_v_infile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__infile, __pyx_v_infile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "ctabix.pyx":836
+ /* "ctabix.pyx":839
*
* self.infile = infile
* if self.infile.closed: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
* self.parser = parser
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__infile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__infile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__closed); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__closed); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_55), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_57), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L3;
}
__pyx_L3:;
- /* "ctabix.pyx":837
+ /* "ctabix.pyx":840
* self.infile = infile
* if self.infile.closed: raise ValueError( "I/O operation on closed file." )
* self.parser = parser # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__parser, __pyx_v_parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__parser, __pyx_v_parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -8465,7 +8533,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_3__iter__(PyObject *_
return __pyx_r;
}
-/* "ctabix.pyx":839
+/* "ctabix.pyx":842
* self.parser = parser
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -8478,7 +8546,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUS
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__iter__", 0);
- /* "ctabix.pyx":840
+ /* "ctabix.pyx":843
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -8510,7 +8578,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_5__next__(PyObject *_
return __pyx_r;
}
-/* "ctabix.pyx":843
+/* "ctabix.pyx":846
*
* # cython version - required for python 3
* def __next__(self): # <<<<<<<<<<<<<<
@@ -8541,7 +8609,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__next__", 0);
- /* "ctabix.pyx":847
+ /* "ctabix.pyx":850
* cdef char * b, * cpy
* cdef size_t nbytes
* while 1: # <<<<<<<<<<<<<<
@@ -8551,33 +8619,33 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
while (1) {
if (!1) break;
- /* "ctabix.pyx":849
+ /* "ctabix.pyx":852
* while 1:
*
* line = self.infile.readline() # <<<<<<<<<<<<<<
* if not line: break
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__infile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__infile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__readline); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__readline); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_line);
__pyx_v_line = __pyx_t_1;
__pyx_t_1 = 0;
- /* "ctabix.pyx":850
+ /* "ctabix.pyx":853
*
* line = self.infile.readline()
* if not line: break # <<<<<<<<<<<<<<
*
* s = _force_bytes( line )
*/
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_line); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_line); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
goto __pyx_L4_break;
@@ -8585,40 +8653,40 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
}
__pyx_L5:;
- /* "ctabix.pyx":852
+ /* "ctabix.pyx":855
* if not line: break
*
* s = _force_bytes( line ) # <<<<<<<<<<<<<<
* b = s
* nbytes = len( line )
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_6ctabix__force_bytes(__pyx_v_line)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_6ctabix__force_bytes(__pyx_v_line)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF(((PyObject *)__pyx_v_s));
__pyx_v_s = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "ctabix.pyx":853
+ /* "ctabix.pyx":856
*
* s = _force_bytes( line )
* b = s # <<<<<<<<<<<<<<
* nbytes = len( line )
* assert b[nbytes] == '\0'
*/
- __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_s)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_s)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_b = __pyx_t_5;
- /* "ctabix.pyx":854
+ /* "ctabix.pyx":857
* s = _force_bytes( line )
* b = s
* nbytes = len( line ) # <<<<<<<<<<<<<<
* assert b[nbytes] == '\0'
*
*/
- __pyx_t_6 = PyObject_Length(__pyx_v_line); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Length(__pyx_v_line); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_nbytes = __pyx_t_6;
- /* "ctabix.pyx":855
+ /* "ctabix.pyx":858
* b = s
* nbytes = len( line )
* assert b[nbytes] == '\0' # <<<<<<<<<<<<<<
@@ -8628,11 +8696,11 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
#ifndef CYTHON_WITHOUT_ASSERTIONS
if (unlikely(!((__pyx_v_b[__pyx_v_nbytes]) == '\x00'))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "ctabix.pyx":858
+ /* "ctabix.pyx":861
*
* # skip comments
* if (b[0] == '#'): continue # <<<<<<<<<<<<<<
@@ -8646,7 +8714,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
}
__pyx_L6:;
- /* "ctabix.pyx":861
+ /* "ctabix.pyx":864
*
* # skip empty lines
* if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # <<<<<<<<<<<<<<
@@ -8672,7 +8740,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
}
__pyx_L7:;
- /* "ctabix.pyx":864
+ /* "ctabix.pyx":867
*
* # make sure that entry is complete
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # <<<<<<<<<<<<<<
@@ -8688,31 +8756,31 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
}
if (__pyx_t_8) {
- /* "ctabix.pyx":865
+ /* "ctabix.pyx":868
* # make sure that entry is complete
* if b[nbytes-1] != '\n' and b[nbytes-1] != '\r':
* raise ValueError( "incomplete line at %s" % line ) # <<<<<<<<<<<<<<
*
* # create a copy
*/
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_52), __pyx_v_line); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), __pyx_v_line); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
}
__pyx_L8:;
- /* "ctabix.pyx":868
+ /* "ctabix.pyx":871
*
* # create a copy
* cpy = <char*>malloc(nbytes+1) # <<<<<<<<<<<<<<
@@ -8721,7 +8789,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
*/
__pyx_v_cpy = ((char *)malloc((__pyx_v_nbytes + 1)));
- /* "ctabix.pyx":869
+ /* "ctabix.pyx":872
* # create a copy
* cpy = <char*>malloc(nbytes+1)
* if cpy == NULL: raise MemoryError() # <<<<<<<<<<<<<<
@@ -8730,12 +8798,12 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
*/
__pyx_t_8 = (__pyx_v_cpy == NULL);
if (__pyx_t_8) {
- PyErr_NoMemory(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_NoMemory(); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L9;
}
__pyx_L9:;
- /* "ctabix.pyx":870
+ /* "ctabix.pyx":873
* cpy = <char*>malloc(nbytes+1)
* if cpy == NULL: raise MemoryError()
* memcpy( cpy, b, nbytes+1) # <<<<<<<<<<<<<<
@@ -8744,7 +8812,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
*/
memcpy(__pyx_v_cpy, __pyx_v_b, (__pyx_v_nbytes + 1));
- /* "ctabix.pyx":872
+ /* "ctabix.pyx":875
* memcpy( cpy, b, nbytes+1)
*
* return self.parser(cpy, nbytes) # <<<<<<<<<<<<<<
@@ -8752,13 +8820,13 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parser); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parser); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_cpy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_cpy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_9 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
@@ -8766,7 +8834,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_2 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
@@ -8777,7 +8845,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
}
__pyx_L4_break:;
- /* "ctabix.pyx":874
+ /* "ctabix.pyx":877
* return self.parser(cpy, nbytes)
*
* raise StopIteration # <<<<<<<<<<<<<<
@@ -8785,7 +8853,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUS
* # python version - required for python 2.7
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -8817,7 +8885,7 @@ static PyObject *__pyx_pw_6ctabix_22tabix_generic_iterator_7next(PyObject *__pyx
return __pyx_r;
}
-/* "ctabix.pyx":877
+/* "ctabix.pyx":880
*
* # python version - required for python 2.7
* def next(self): # <<<<<<<<<<<<<<
@@ -8835,7 +8903,7 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED P
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("next", 0);
- /* "ctabix.pyx":878
+ /* "ctabix.pyx":881
* # python version - required for python 2.7
* def next(self):
* return self.__next__() # <<<<<<<<<<<<<<
@@ -8843,9 +8911,9 @@ static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED P
* def tabix_iterator( infile, parser ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____next__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____next__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = __pyx_t_2;
@@ -8895,11 +8963,11 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject
case 1:
if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "tabix_iterator") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "tabix_iterator") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -8912,7 +8980,7 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("ctabix.tabix_iterator", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -8923,7 +8991,7 @@ static PyObject *__pyx_pw_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject
return __pyx_r;
}
-/* "ctabix.pyx":880
+/* "ctabix.pyx":883
* return self.__next__()
*
* def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<<
@@ -8942,7 +9010,7 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("tabix_iterator", 0);
- /* "ctabix.pyx":882
+ /* "ctabix.pyx":885
* def tabix_iterator( infile, parser ):
* """return an iterator over all entries in a file."""
* return tabix_generic_iterator( infile, parser ) # <<<<<<<<<<<<<<
@@ -8950,9 +9018,9 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_
* # used to be: isinstance( infile, file):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s_56); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s_58); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_infile);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_infile);
@@ -8960,7 +9028,7 @@ static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_
__Pyx_INCREF(__pyx_v_parser);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_parser);
__Pyx_GIVEREF(__pyx_v_parser);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -9026,9 +9094,9 @@ static PyMethodDef __pyx_methods_6ctabix_Tabixfile[] = {
};
static struct PyGetSetDef __pyx_getsets_6ctabix_Tabixfile[] = {
- {(char *)"filename", __pyx_getprop_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_57), 0},
- {(char *)"header", __pyx_getprop_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_58), 0},
- {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_59), 0},
+ {(char *)"filename", __pyx_getprop_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_59), 0},
+ {(char *)"header", __pyx_getprop_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_60), 0},
+ {(char *)"contigs", __pyx_getprop_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_61), 0},
{0, 0, 0, 0, 0}
};
@@ -10386,6 +10454,7 @@ static PyObject *__pyx_tp_new_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObj
static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) {
struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
@@ -10396,6 +10465,7 @@ static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) {
PyErr_Restore(etype, eval, etb);
}
Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -10592,6 +10662,7 @@ static PyObject *__pyx_tp_new_6ctabix_tabix_inplace_iterator(PyTypeObject *t, Py
static void __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator(PyObject *o) {
struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
@@ -10602,6 +10673,7 @@ static void __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator(PyObject *o) {
PyErr_Restore(etype, eval, etb);
}
Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -10798,7 +10870,9 @@ static PyObject *__pyx_tp_new_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObj
static void __pyx_tp_dealloc_6ctabix_tabix_copy_iterator(PyObject *o) {
struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o;
+ PyObject_GC_UnTrack(o);
Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -11021,17 +11095,18 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_43, __pyx_k_43, sizeof(__pyx_k_43), 0, 0, 1, 0},
{&__pyx_kp_s_45, __pyx_k_45, sizeof(__pyx_k_45), 0, 0, 1, 0},
{&__pyx_kp_s_47, __pyx_k_47, sizeof(__pyx_k_47), 0, 0, 1, 0},
- {&__pyx_kp_s_48, __pyx_k_48, sizeof(__pyx_k_48), 0, 0, 1, 0},
{&__pyx_kp_s_49, __pyx_k_49, sizeof(__pyx_k_49), 0, 0, 1, 0},
{&__pyx_kp_s_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 0, 1, 0},
- {&__pyx_kp_s_52, __pyx_k_52, sizeof(__pyx_k_52), 0, 0, 1, 0},
- {&__pyx_n_s_56, __pyx_k_56, sizeof(__pyx_k_56), 0, 0, 1, 1},
+ {&__pyx_kp_s_50, __pyx_k_50, sizeof(__pyx_k_50), 0, 0, 1, 0},
+ {&__pyx_kp_s_51, __pyx_k_51, sizeof(__pyx_k_51), 0, 0, 1, 0},
+ {&__pyx_kp_s_54, __pyx_k_54, sizeof(__pyx_k_54), 0, 0, 1, 0},
+ {&__pyx_n_s_58, __pyx_k_58, sizeof(__pyx_k_58), 0, 0, 1, 1},
{&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
- {&__pyx_n_s_60, __pyx_k_60, sizeof(__pyx_k_60), 0, 0, 1, 1},
- {&__pyx_kp_s_63, __pyx_k_63, sizeof(__pyx_k_63), 0, 0, 1, 0},
+ {&__pyx_n_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 1},
+ {&__pyx_kp_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 0},
{&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
- {&__pyx_kp_s_74, __pyx_k_74, sizeof(__pyx_k_74), 0, 0, 1, 0},
- {&__pyx_n_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 1},
+ {&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0},
+ {&__pyx_n_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 1},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
{&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
{&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
@@ -11140,9 +11215,9 @@ static int __Pyx_InitCachedBuiltins(void) {
__pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_OSError = __Pyx_GetName(__pyx_b, __pyx_n_s__OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_ord = __Pyx_GetName(__pyx_b, __pyx_n_s__ord); if (!__pyx_builtin_ord) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_MemoryError = __Pyx_GetName(__pyx_b, __pyx_n_s__MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_ord = __Pyx_GetName(__pyx_b, __pyx_n_s__ord); if (!__pyx_builtin_ord) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_MemoryError = __Pyx_GetName(__pyx_b, __pyx_n_s__MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -11354,103 +11429,117 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_36));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_38));
- /* "ctabix.pyx":655
- * if not os.path.exists(filename): raise IOError("No such file '%s'" % filename)
+ /* "ctabix.pyx":656
*
- * if not filename.endswith(".gz"): # <<<<<<<<<<<<<<
- * tabix_compress( filename, filename + ".gz", force = force )
- * os.unlink( filename )
+ * if preset == None and (seq_col == None or start_col == None or end_col == None):
+ * raise ValueError("neither preset nor seq_col,start_col and end_col given" ) # <<<<<<<<<<<<<<
+ *
+ * if not filename.endswith(".gz"):
*/
- __pyx_k_tuple_44 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_44 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_44);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_43));
PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, ((PyObject *)__pyx_kp_s_43));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
- /* "ctabix.pyx":661
+ /* "ctabix.pyx":658
+ * raise ValueError("neither preset nor seq_col,start_col and end_col given" )
*
- * if not force and os.path.exists(filename + ".tbi" ):
- * raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" ) # <<<<<<<<<<<<<<
- *
- * # columns (1-based)
+ * if not filename.endswith(".gz"): # <<<<<<<<<<<<<<
+ * tabix_compress( filename, filename + ".gz", force = force )
+ * os.unlink( filename )
*/
- __pyx_k_tuple_46 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_46 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_46);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_45));
PyTuple_SET_ITEM(__pyx_k_tuple_46, 0, ((PyObject *)__pyx_kp_s_45));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_45));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_46));
- /* "ctabix.pyx":719
+ /* "ctabix.pyx":664
+ *
+ * if not force and os.path.exists(filename + ".tbi" ):
+ * raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" ) # <<<<<<<<<<<<<<
+ *
+ * # columns (1-based)
+ */
+ __pyx_k_tuple_48 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_48);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_47));
+ PyTuple_SET_ITEM(__pyx_k_tuple_48, 0, ((PyObject *)__pyx_kp_s_47));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_47));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48));
+
+ /* "ctabix.pyx":722
*
* cdef int fd = PyObject_AsFileDescriptor( infile )
* if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
* self.infile = fdopen( fd, 'r')
*
*/
- __pyx_k_tuple_50 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_50);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_49));
- PyTuple_SET_ITEM(__pyx_k_tuple_50, 0, ((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_50));
+ __pyx_k_tuple_52 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_52);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
+ PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, ((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
- /* "ctabix.pyx":722
+ /* "ctabix.pyx":725
* self.infile = fdopen( fd, 'r')
*
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
*
* self.buffer = <char*>malloc( buffer_size )
*/
- __pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_51);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_49));
- PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, ((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
+ __pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_53);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
+ PyTuple_SET_ITEM(__pyx_k_tuple_53, 0, ((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
- /* "ctabix.pyx":780
+ /* "ctabix.pyx":783
*
* cdef int fd = PyObject_AsFileDescriptor( infile )
* if fd == -1: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
* self.infile = fdopen( fd, 'r')
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
*/
- __pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_53);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_49));
- PyTuple_SET_ITEM(__pyx_k_tuple_53, 0, ((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
+ __pyx_k_tuple_55 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_55);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
+ PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, ((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
- /* "ctabix.pyx":782
+ /* "ctabix.pyx":785
* if fd == -1: raise ValueError( "I/O operation on closed file." )
* self.infile = fdopen( fd, 'r')
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
* self.parser = parser
*
*/
- __pyx_k_tuple_54 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_54)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_54);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_49));
- PyTuple_SET_ITEM(__pyx_k_tuple_54, 0, ((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_54));
+ __pyx_k_tuple_56 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_56);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
+ PyTuple_SET_ITEM(__pyx_k_tuple_56, 0, ((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_56));
- /* "ctabix.pyx":836
+ /* "ctabix.pyx":839
*
* self.infile = infile
* if self.infile.closed: raise ValueError( "I/O operation on closed file." ) # <<<<<<<<<<<<<<
* self.parser = parser
*
*/
- __pyx_k_tuple_55 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_55);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_49));
- PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, ((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_49));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
+ __pyx_k_tuple_57 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_57);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
+ PyTuple_SET_ITEM(__pyx_k_tuple_57, 0, ((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
/* "ctabix.pyx":564
* ti_iter_destroy(self.iterator)
@@ -11459,43 +11548,43 @@ static int __Pyx_InitCachedConstants(void) {
* filename_out,
* force = False ):
*/
- __pyx_k_tuple_61 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_61);
+ __pyx_k_tuple_63 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_63);
__Pyx_INCREF(((PyObject *)__pyx_n_s__filename_in));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 0, ((PyObject *)__pyx_n_s__filename_in));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 0, ((PyObject *)__pyx_n_s__filename_in));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename_in));
__Pyx_INCREF(((PyObject *)__pyx_n_s__filename_out));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 1, ((PyObject *)__pyx_n_s__filename_out));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 1, ((PyObject *)__pyx_n_s__filename_out));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename_out));
__Pyx_INCREF(((PyObject *)__pyx_n_s__force));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 2, ((PyObject *)__pyx_n_s__force));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 2, ((PyObject *)__pyx_n_s__force));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__force));
__Pyx_INCREF(((PyObject *)__pyx_n_s__WINDOW_SIZE));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 3, ((PyObject *)__pyx_n_s__WINDOW_SIZE));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 3, ((PyObject *)__pyx_n_s__WINDOW_SIZE));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__WINDOW_SIZE));
__Pyx_INCREF(((PyObject *)__pyx_n_s__c));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 4, ((PyObject *)__pyx_n_s__c));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 4, ((PyObject *)__pyx_n_s__c));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__c));
__Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 5, ((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 5, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
__Pyx_INCREF(((PyObject *)__pyx_n_s__buffer));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 6, ((PyObject *)__pyx_n_s__buffer));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 6, ((PyObject *)__pyx_n_s__buffer));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__buffer));
__Pyx_INCREF(((PyObject *)__pyx_n_s__fp));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 7, ((PyObject *)__pyx_n_s__fp));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 7, ((PyObject *)__pyx_n_s__fp));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__fp));
__Pyx_INCREF(((PyObject *)__pyx_n_s__fd_src));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 8, ((PyObject *)__pyx_n_s__fd_src));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 8, ((PyObject *)__pyx_n_s__fd_src));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd_src));
__Pyx_INCREF(((PyObject *)__pyx_n_s__O_RDONLY));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 9, ((PyObject *)__pyx_n_s__O_RDONLY));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 9, ((PyObject *)__pyx_n_s__O_RDONLY));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__O_RDONLY));
__Pyx_INCREF(((PyObject *)__pyx_n_s__fn));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 10, ((PyObject *)__pyx_n_s__fn));
+ PyTuple_SET_ITEM(__pyx_k_tuple_63, 10, ((PyObject *)__pyx_n_s__fn));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__fn));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
- __pyx_k_codeobj_62 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_63, __pyx_n_s__tabix_compress, 564, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
+ __pyx_k_codeobj_64 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_compress, 564, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "ctabix.pyx":611
* if r < 0: raise OSError("writing failed")
@@ -11504,145 +11593,145 @@ static int __Pyx_InitCachedConstants(void) {
* force = False,
* seq_col = None,
*/
- __pyx_k_tuple_64 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_64);
+ __pyx_k_tuple_66 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_66);
__Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 0, ((PyObject *)__pyx_n_s__filename));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 0, ((PyObject *)__pyx_n_s__filename));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
__Pyx_INCREF(((PyObject *)__pyx_n_s__force));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 1, ((PyObject *)__pyx_n_s__force));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 1, ((PyObject *)__pyx_n_s__force));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__force));
__Pyx_INCREF(((PyObject *)__pyx_n_s__seq_col));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 2, ((PyObject *)__pyx_n_s__seq_col));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 2, ((PyObject *)__pyx_n_s__seq_col));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__seq_col));
__Pyx_INCREF(((PyObject *)__pyx_n_s__start_col));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 3, ((PyObject *)__pyx_n_s__start_col));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 3, ((PyObject *)__pyx_n_s__start_col));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__start_col));
__Pyx_INCREF(((PyObject *)__pyx_n_s__end_col));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 4, ((PyObject *)__pyx_n_s__end_col));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 4, ((PyObject *)__pyx_n_s__end_col));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__end_col));
__Pyx_INCREF(((PyObject *)__pyx_n_s__preset));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 5, ((PyObject *)__pyx_n_s__preset));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 5, ((PyObject *)__pyx_n_s__preset));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__preset));
__Pyx_INCREF(((PyObject *)__pyx_n_s__meta_char));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 6, ((PyObject *)__pyx_n_s__meta_char));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 6, ((PyObject *)__pyx_n_s__meta_char));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__meta_char));
__Pyx_INCREF(((PyObject *)__pyx_n_s__zerobased));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 7, ((PyObject *)__pyx_n_s__zerobased));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 7, ((PyObject *)__pyx_n_s__zerobased));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__zerobased));
__Pyx_INCREF(((PyObject *)__pyx_n_s__preset2conf));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 8, ((PyObject *)__pyx_n_s__preset2conf));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 8, ((PyObject *)__pyx_n_s__preset2conf));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__preset2conf));
__Pyx_INCREF(((PyObject *)__pyx_n_s__conf_data));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 9, ((PyObject *)__pyx_n_s__conf_data));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 9, ((PyObject *)__pyx_n_s__conf_data));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__conf_data));
__Pyx_INCREF(((PyObject *)__pyx_n_s__conf));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 10, ((PyObject *)__pyx_n_s__conf));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 10, ((PyObject *)__pyx_n_s__conf));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__conf));
__Pyx_INCREF(((PyObject *)__pyx_n_s__fn));
- PyTuple_SET_ITEM(__pyx_k_tuple_64, 11, ((PyObject *)__pyx_n_s__fn));
+ PyTuple_SET_ITEM(__pyx_k_tuple_66, 11, ((PyObject *)__pyx_n_s__fn));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__fn));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_64));
- __pyx_k_codeobj_65 = (PyObject*)__Pyx_PyCode_New(8, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_64, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_63, __pyx_n_s__tabix_index, 611, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_66));
+ __pyx_k_codeobj_67 = (PyObject*)__Pyx_PyCode_New(8, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_index, 611, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "ctabix.pyx":833
+ /* "ctabix.pyx":836
* Permits the use of file-like objects for example from the gzip module.
* '''
* def __init__(self, infile, parser ): # <<<<<<<<<<<<<<
*
* self.infile = infile
*/
- __pyx_k_tuple_66 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_66);
+ __pyx_k_tuple_68 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_68);
__Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_66, 0, ((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_68, 0, ((PyObject *)__pyx_n_s__self));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
__Pyx_INCREF(((PyObject *)__pyx_n_s__infile));
- PyTuple_SET_ITEM(__pyx_k_tuple_66, 1, ((PyObject *)__pyx_n_s__infile));
+ PyTuple_SET_ITEM(__pyx_k_tuple_68, 1, ((PyObject *)__pyx_n_s__infile));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__infile));
__Pyx_INCREF(((PyObject *)__pyx_n_s__parser));
- PyTuple_SET_ITEM(__pyx_k_tuple_66, 2, ((PyObject *)__pyx_n_s__parser));
+ PyTuple_SET_ITEM(__pyx_k_tuple_68, 2, ((PyObject *)__pyx_n_s__parser));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__parser));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_66));
- __pyx_k_codeobj_67 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_66, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_63, __pyx_n_s____init__, 833, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68));
+ __pyx_k_codeobj_69 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____init__, 836, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "ctabix.pyx":839
+ /* "ctabix.pyx":842
* self.parser = parser
*
* def __iter__(self): # <<<<<<<<<<<<<<
* return self
*
*/
- __pyx_k_tuple_68 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_68);
+ __pyx_k_tuple_70 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_70);
__Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_68, 0, ((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_70, 0, ((PyObject *)__pyx_n_s__self));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68));
- __pyx_k_codeobj_69 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_63, __pyx_n_s____iter__, 839, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_70));
+ __pyx_k_codeobj_71 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____iter__, 842, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "ctabix.pyx":843
+ /* "ctabix.pyx":846
*
* # cython version - required for python 3
* def __next__(self): # <<<<<<<<<<<<<<
*
* cdef char * b, * cpy
*/
- __pyx_k_tuple_70 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_70);
+ __pyx_k_tuple_72 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_72);
__Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_70, 0, ((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_72, 0, ((PyObject *)__pyx_n_s__self));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
__Pyx_INCREF(((PyObject *)__pyx_n_s__b));
- PyTuple_SET_ITEM(__pyx_k_tuple_70, 1, ((PyObject *)__pyx_n_s__b));
+ PyTuple_SET_ITEM(__pyx_k_tuple_72, 1, ((PyObject *)__pyx_n_s__b));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__b));
__Pyx_INCREF(((PyObject *)__pyx_n_s__cpy));
- PyTuple_SET_ITEM(__pyx_k_tuple_70, 2, ((PyObject *)__pyx_n_s__cpy));
+ PyTuple_SET_ITEM(__pyx_k_tuple_72, 2, ((PyObject *)__pyx_n_s__cpy));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__cpy));
__Pyx_INCREF(((PyObject *)__pyx_n_s__nbytes));
- PyTuple_SET_ITEM(__pyx_k_tuple_70, 3, ((PyObject *)__pyx_n_s__nbytes));
+ PyTuple_SET_ITEM(__pyx_k_tuple_72, 3, ((PyObject *)__pyx_n_s__nbytes));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__nbytes));
__Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_70, 4, ((PyObject *)__pyx_n_s__line));
+ PyTuple_SET_ITEM(__pyx_k_tuple_72, 4, ((PyObject *)__pyx_n_s__line));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
__Pyx_INCREF(((PyObject *)__pyx_n_s__s));
- PyTuple_SET_ITEM(__pyx_k_tuple_70, 5, ((PyObject *)__pyx_n_s__s));
+ PyTuple_SET_ITEM(__pyx_k_tuple_72, 5, ((PyObject *)__pyx_n_s__s));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__s));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_70));
- __pyx_k_codeobj_71 = (PyObject*)__Pyx_PyCode_New(1, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_63, __pyx_n_s____next__, 843, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
+ __pyx_k_codeobj_73 = (PyObject*)__Pyx_PyCode_New(1, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____next__, 846, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "ctabix.pyx":877
+ /* "ctabix.pyx":880
*
* # python version - required for python 2.7
* def next(self): # <<<<<<<<<<<<<<
* return self.__next__()
*
*/
- __pyx_k_tuple_72 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_72);
+ __pyx_k_tuple_74 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_74);
__Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_72, 0, ((PyObject *)__pyx_n_s__self));
+ PyTuple_SET_ITEM(__pyx_k_tuple_74, 0, ((PyObject *)__pyx_n_s__self));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
- __pyx_k_codeobj_73 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_63, __pyx_n_s__next, 877, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_74));
+ __pyx_k_codeobj_75 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__next, 880, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "ctabix.pyx":880
+ /* "ctabix.pyx":883
* return self.__next__()
*
* def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<<
* """return an iterator over all entries in a file."""
* return tabix_generic_iterator( infile, parser )
*/
- __pyx_k_tuple_75 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_75);
+ __pyx_k_tuple_77 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_77);
__Pyx_INCREF(((PyObject *)__pyx_n_s__infile));
- PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_n_s__infile));
+ PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_n_s__infile));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__infile));
__Pyx_INCREF(((PyObject *)__pyx_n_s__parser));
- PyTuple_SET_ITEM(__pyx_k_tuple_75, 1, ((PyObject *)__pyx_n_s__parser));
+ PyTuple_SET_ITEM(__pyx_k_tuple_77, 1, ((PyObject *)__pyx_n_s__parser));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__parser));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
- __pyx_k_codeobj_76 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_63, __pyx_n_s__tabix_iterator, 880, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
+ __pyx_k_codeobj_78 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_77, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_iterator, 883, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -11717,6 +11806,14 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__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, "ctabix")) {
+ if (unlikely(PyDict_SetItemString(modules, "ctabix", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ }
+ #endif
__pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_PYPY
Py_INCREF(__pyx_b);
@@ -11799,15 +11896,15 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__pyx_ptype_6ctabix_TabixIteratorParsed = &__pyx_type_6ctabix_TabixIteratorParsed;
__pyx_vtabptr_6ctabix_tabix_inplace_iterator = &__pyx_vtable_6ctabix_tabix_inplace_iterator;
__pyx_vtable_6ctabix_tabix_inplace_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *))__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__;
- if (PyType_Ready(&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_tabix_inplace_iterator = &__pyx_type_6ctabix_tabix_inplace_iterator;
__pyx_vtabptr_6ctabix_tabix_copy_iterator = &__pyx_vtable_6ctabix_tabix_copy_iterator;
__pyx_vtable_6ctabix_tabix_copy_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_copy_iterator *))__pyx_f_6ctabix_19tabix_copy_iterator___cnext__;
- if (PyType_Ready(&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_6ctabix_tabix_copy_iterator = &__pyx_type_6ctabix_tabix_copy_iterator;
/*--- Type import code ---*/
__pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11906,7 +12003,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
*/
__pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s_60); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s_62); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -12043,98 +12140,98 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_index, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "ctabix.pyx":828
+ /* "ctabix.pyx":831
* return self.__cnext__()
*
* class tabix_generic_iterator: # <<<<<<<<<<<<<<
* '''iterate over ``infile``.
*
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "ctabix.pyx":833
+ /* "ctabix.pyx":836
* Permits the use of file-like objects for example from the gzip module.
* '''
* def __init__(self, infile, parser ): # <<<<<<<<<<<<<<
*
* self.infile = infile
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_1__init__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_67)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_1__init__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_69)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "ctabix.pyx":839
+ /* "ctabix.pyx":842
* self.parser = parser
*
* def __iter__(self): # <<<<<<<<<<<<<<
* return self
*
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_3__iter__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_69)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_3__iter__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_71)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____iter__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____iter__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "ctabix.pyx":843
+ /* "ctabix.pyx":846
*
* # cython version - required for python 3
* def __next__(self): # <<<<<<<<<<<<<<
*
* cdef char * b, * cpy
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_5__next__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_71)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_5__next__, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_73)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____next__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____next__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "ctabix.pyx":877
+ /* "ctabix.pyx":880
*
* # python version - required for python 2.7
* def next(self): # <<<<<<<<<<<<<<
* return self.__next__()
*
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_7next, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_73)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_6ctabix_22tabix_generic_iterator_7next, 0, NULL, __pyx_n_s__ctabix, ((PyObject *)__pyx_k_codeobj_75)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__next, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__next, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "ctabix.pyx":828
+ /* "ctabix.pyx":831
* return self.__cnext__()
*
* class tabix_generic_iterator: # <<<<<<<<<<<<<<
* '''iterate over ``infile``.
*
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_74)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s_56, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_76)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s_58, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s_56, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s_58, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "ctabix.pyx":880
+ /* "ctabix.pyx":883
* return self.__next__()
*
* def tabix_iterator( infile, parser ): # <<<<<<<<<<<<<<
* """return an iterator over all entries in a file."""
* return tabix_generic_iterator( infile, parser )
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_6ctabix_5tabix_iterator, NULL, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_6ctabix_5tabix_iterator, NULL, __pyx_n_s__ctabix); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_iterator, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_iterator, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "ctabix.pyx":896
+ /* "ctabix.pyx":899
* # return tabix_generic_iterator( infile, parser )
*
* __all__ = ["tabix_index", # <<<<<<<<<<<<<<
* "tabix_compress",
* "Tabixfile",
*/
- __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_index));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tabix_index));
@@ -12160,10 +12257,10 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_iterator));
PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__tabix_iterator));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__tabix_iterator));
- __Pyx_INCREF(((PyObject *)__pyx_n_s_77));
- PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_77));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s_77));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(((PyObject *)__pyx_n_s_79));
+ PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_79));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s_79));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
/* "ctabix.pyx":1
@@ -13285,6 +13382,10 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
else
return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
int32_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
@@ -13304,6 +13405,7 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
if (likely(!ret))
return val;
}
+ #endif
return (int32_t)-1;
}
}
diff --git a/pysam/ctabix.pyx b/pysam/ctabix.pyx
index a522676..6a19541 100644
--- a/pysam/ctabix.pyx
+++ b/pysam/ctabix.pyx
@@ -652,6 +652,9 @@ def tabix_index( filename,
if not os.path.exists(filename): raise IOError("No such file '%s'" % filename)
+ if preset == None and (seq_col == None or start_col == None or end_col == None):
+ raise ValueError("neither preset nor seq_col,start_col and end_col given" )
+
if not filename.endswith(".gz"):
tabix_compress( filename, filename + ".gz", force = force )
os.unlink( filename )
diff --git a/pysam/cvcf.c b/pysam/cvcf.c
index 6caaba0..6243139 100644
--- a/pysam/cvcf.c
+++ b/pysam/cvcf.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Mon Nov 19 08:44:41 2012 */
+/* Generated by Cython 0.16 on Tue Nov 6 12:17:11 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -461,8 +461,8 @@ struct __pyx_obj_10TabProxies_TupleProxy {
};
-/* "TabProxies.pxd":69
- * cdef char * getAttributes( self )
+/* "TabProxies.pxd":68
+ * cdef int getMaxFields( self, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
* pass
@@ -473,7 +473,7 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy {
};
-/* "TabProxies.pxd":72
+/* "TabProxies.pxd":71
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
@@ -519,7 +519,7 @@ struct __pyx_obj_4cvcf_VCFRecord {
};
-/* "TabProxies.pxd":83
+/* "TabProxies.pxd":82
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
@@ -753,8 +753,8 @@ struct __pyx_vtabstruct_10TabProxies_TupleProxy {
static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
-/* "TabProxies.pxd":69
- * cdef char * getAttributes( self )
+/* "TabProxies.pxd":68
+ * cdef int getMaxFields( self, size_t nbytes )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
* pass
@@ -767,7 +767,7 @@ struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
-/* "TabProxies.pxd":83
+/* "TabProxies.pxd":82
* cdef update( self, char * buffer, size_t nbytes )
*
* cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
@@ -805,7 +805,6 @@ static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ct
struct __pyx_vtabstruct_10TabProxies_GTFProxy {
struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
- char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *);
};
static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
@@ -824,7 +823,7 @@ struct __pyx_vtabstruct_4cvcf_VCFRecord {
static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
-/* "TabProxies.pxd":72
+/* "TabProxies.pxd":71
* pass
*
* cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
@@ -1468,7 +1467,7 @@ static char __pyx_k_125[] = "Invalid error string: %s";
static char __pyx_k_126[] = "needs to be checked";
static char __pyx_k_128[] = "[|/\\\\]";
static char __pyx_k_130[] = "^[ACGTN]+$";
-static char __pyx_k_134[] = "/ifs/devel/pysam/pysam/cvcf.pyx";
+static char __pyx_k_134[] = "/home/andreas/devel/pysam/pysam/cvcf.pyx";
static char __pyx_k_137[] = "id numbertype number type description missingvalue";
static char __pyx_k_139[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
static char __pyx_k_140[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
@@ -26499,12 +26498,12 @@ PyMODINIT_FUNC PyInit_cvcf(void)
__pyx_vtabptr_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
diff --git a/pysam/version.py b/pysam/version.py
index 6755f3d..7e6b192 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,6 +1,6 @@
# pysam versioning information
-__version__ = "0.7"
+__version__ = "0.7.1"
__samtools_version__ = "0.1.18"
diff --git a/setup.cfg b/setup.cfg
index b9711b8..81d163a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,8 +1,8 @@
[bdist_rpm]
-doc_files = README doc/*.html ChangeLog
vendor = TDB
-packager = TDB <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 979b936..a1b8de8 100644
--- a/setup.py
+++ b/setup.py
@@ -114,14 +114,30 @@ if len(sys.argv) >= 2 and sys.argv[1] == "refresh":
sys.exit(0)
-
-
from distribute_setup import use_setuptools
use_setuptools()
from setuptools import Extension, setup
-from Cython.Distutils import build_ext
+#######################################################
+#######################################################
+try:
+ from Cython.Distutils import build_ext
+except ImportError:
+ # no Cython available - use existing C code
+ cmdclass = { }
+ csamtools_sources = [ "pysam/csamtools.c" ]
+ tabix_sources = [ "pysam/tabix.c" ]
+ tabproxies_sourcess = ["pysam/TabProxies.c" ]
+ cvcf_sources = ["pysam/cvcf.c" ]
+else:
+ cmdclass = { 'build_ext' : build_ext }
+ csamtools_sources = [ "pysam/csamtools.pyx" ]
+ tabix_sources = [ "pysam/ctabix.pyx" ]
+ tabproxies_sources = ["pysam/TabProxies.pyx" ]
+ cvcf_sources = ["pysam/cvcf.pyx" ]
+
+#######################################################
classifiers = """
Development Status :: 2 - Alpha
Operating System :: MacOS :: MacOS X
@@ -135,6 +151,8 @@ Topic :: Scientific/Engineering
Topic :: Scientific/Engineering :: Bioinformatics
"""
+#######################################################
+## Windows compatibility
if platform.system()=='Windows':
include_os = ['win32']
os_c_files = ['win32/getopt.c']
@@ -142,9 +160,10 @@ else:
include_os = []
os_c_files = []
+#######################################################
samtools = Extension(
- "csamtools", # name of extension
- [ "pysam/csamtools.pyx" ] +\
+ "csamtools",
+ csamtools_sources +\
[ "pysam/%s" % x for x in (
"pysam_util.c", )] +\
glob.glob( os.path.join( "samtools", "*.pysam.c" )) +\
@@ -159,8 +178,8 @@ samtools = Extension(
)
tabix = Extension(
- "ctabix", # name of extension
- [ "pysam/ctabix.pyx", ] +\
+ "ctabix",
+ tabix_sources +\
[ "pysam/%s" % x for x in ( "tabix_util.c", )] +\
os_c_files + \
glob.glob( os.path.join( "tabix", "*.pysam.c" ) ),
@@ -173,8 +192,8 @@ tabix = Extension(
)
tabproxies = Extension(
- "TabProxies", # name of extension
- [ "pysam/TabProxies.pyx", ] + os_c_files,
+ "TabProxies",
+ tabproxies_sources + os_c_files,
library_dirs=[],
include_dirs= include_os,
libraries=[ "z", ],
@@ -182,8 +201,8 @@ tabproxies = Extension(
)
cvcf = Extension(
- "cvcf", # name of extension
- [ "pysam/cvcf.pyx", ] + os_c_files,
+ "cvcf",
+ cvcf_sources + os_c_files,
library_dirs=[],
include_dirs= ["tabix",] + include_os,
libraries=[ "z", ],
@@ -207,7 +226,7 @@ metadata = {
# cython larger that 0.16 for yield support
'requires' : ['cython (>=0.16)'],
'ext_modules': [samtools, tabix, tabproxies, cvcf ],
- 'cmdclass' : {'build_ext': build_ext},
+ 'cmdclass' : cmdclass,
'install_requires' : ['cython>=0.12.1',],
# do not pack in order to permit linking to csamtools.so
'zip_safe' :False,
diff --git a/tests/example_btag.bam b/tests/example_btag.bam
new file mode 100644
index 0000000..7cd5c0c
Binary files /dev/null and b/tests/example_btag.bam differ
diff --git a/tests/pysam_test.py b/tests/pysam_test.py
index 3407182..c8acf83 100755
--- a/tests/pysam_test.py
+++ b/tests/pysam_test.py
@@ -891,6 +891,16 @@ class TestHeaderBam(TestHeaderSam):
self.samfile=pysam.Samfile( "ex3.bam","rb" )
+class TestHeader1000Genomes( unittest.TestCase ):
+
+ bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam"
+
+ def testRead( self ):
+
+ f = pysam.Samfile( self.bamfile, "rb" )
+ data = f.header.copy()
+ self.assertTrue( data )
+
class TestUnmappedReads(unittest.TestCase):
def testSAM(self):
--
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/pysam.git
More information about the debian-med-commit
mailing list