New upstream version 0.15.2+ds (804729d0) · Commits · Debian Med / python-pysam

.travis.yml

+0 −1

Original line number	Diff line number	Diff line
		@@ -3,7 +3,6 @@ os:
		- osx

		language: c
		sudo: false

		env:
		matrix:

MANIFEST.in

+2 −2

Original line number	Diff line number	Diff line
		@@ -50,8 +50,8 @@ include htslib/htslib.pc.in
		include htslib/htslib/*.h
		include htslib/cram/*.c
		include htslib/cram/*.h
		include htslib/win/*.c
		include htslib/win/*.h
		include htslib/os/*.c
		include htslib/os/*.h
		include cy_build.py
		include pysam.py
		include requirements.txt

NEWS

+11 −0

Original line number	Diff line number	Diff line
		@@ -5,6 +5,17 @@ http://pysam.readthedocs.io/en/latest/release.html
		Release notes
		=============

		Release 0.15.2
		==============

		Bugfix release.

		* [#746] catch pileup itorator out-of-scope segfaults
		* [#747] fix faixd fetch with region
		* [#748] increase max_pos to (1<<31)-1
		* [#645] Add missing macOS stub files in `MANIFEST.in`, @SoapZA
		* [#737] Fix bug in get_aligned_pairs, @bkohrn

		Release 0.15.1
		==============

doc/release.rst

+11 −0

Original line number	Diff line number	Diff line
		@@ -7,6 +7,17 @@ Release 0.15.1

		Bugfix release.

		* [#746] catch pileup itorator out-of-scope segfaults
		* [#747] fix faixd fetch with region
		* [#748] increase max_pos to (1<<31)-1
		* [#645] Add missing macOS stub files in `MANIFEST.in`, @SoapZA
		* [#737] Fix bug in get_aligned_pairs, @bkohrn

		Release 0.15.1
		==============

		Bugfix release.

		* [#716] raise ValueError if tid is out of range when writing
		* [#697] release version using cython 0.28.5 for python 3.7
		compatibility

pysam/libcalignedsegment.pyx

+60 −5

Original line number	Diff line number	Diff line
		@@ -402,6 +402,13 @@ cdef inline pack_tags(tags):
		# use array.tostring() to retrieve byte representation and
		# save as bytes
		datafmt = "2sBBI%is" % (len(value) * DATATYPE2FORMAT[typecode][1])
		if IS_PYTHON3:
		args.extend([pytag[:2],
		ord("B"),
		typecode,
		len(value),
		value.tobytes()])
		else:
		args.extend([pytag[:2],
		ord("B"),
		typecode,
		@@ -1945,6 +1952,8 @@ cdef class AlignedSegment:
		else:
		for i from pos <= i < pos + l:
		result.append((None, i))
		else:
		r_idx += l
		pos += l

		elif op == BAM_CHARD_CLIP:
		@@ -2845,6 +2854,10 @@ cdef class PileupColumn:
		# out of sync.
		for x from 0 <= x < self.n_pu:
		p = &(self.plp[0][x])
		if p == NULL:
		raise ValueError(
		"pileup buffer out of sync - most likely use of iterator "
		"outside loop")
		if pileup_base_qual_skip(p, self.min_base_quality):
		continue
		pileups.append(makePileupRead(p, self.header))
		@@ -2887,8 +2900,15 @@ cdef class PileupColumn:
		cdef uint32_t c = 0
		cdef uint32_t cnt = 0
		cdef bam_pileup1_t * p = NULL
		if self.plp == NULL or self.plp[0] == NULL:
		raise ValueError("PileupColumn accessed after iterator finished")

		for x from 0 <= x < self.n_pu:
		p = &(self.plp[0][x])
		if p == NULL:
		raise ValueError(
		"pileup buffer out of sync - most likely use of iterator "
		"outside loop")
		if pileup_base_qual_skip(p, self.min_base_quality):
		continue
		cnt += 1
		@@ -2957,10 +2977,17 @@ cdef class PileupColumn:
		cdef uint8_t * buf = self.buf
		cdef bam_pileup1_t * p = NULL

		if self.plp == NULL or self.plp[0] == NULL:
		raise ValueError("PileupColumn accessed after iterator finished")

		# todo: reference sequence to count matches/mismatches
		# todo: convert assertions to exceptions
		for x from 0 <= x < self.n_pu:
		p = &(self.plp[0][x])
		if p == NULL:
		raise ValueError(
		"pileup buffer out of sync - most likely use of iterator "
		"outside loop")
		if pileup_base_qual_skip(p, self.min_base_quality):
		continue
		# see samtools pileup_seq
		@@ -3062,6 +3089,11 @@ cdef class PileupColumn:
		result = []
		for x from 0 <= x < self.n_pu:
		p = &(self.plp[0][x])
		if p == NULL:
		raise ValueError(
		"pileup buffer out of sync - most likely use of iterator "
		"outside loop")

		if p.qpos < p.b.core.l_qseq:
		c = bam_get_qual(p.b)[p.qpos]
		else:
		@@ -3079,11 +3111,19 @@ cdef class PileupColumn:

		list: a list of quality scores
		"""
		if self.plp == NULL or self.plp[0] == NULL:
		raise ValueError("PileupColumn accessed after iterator finished")

		cdef uint32_t x = 0
		cdef bam_pileup1_t * p = NULL
		result = []
		for x from 0 <= x < self.n_pu:
		p = &(self.plp[0][x])
		if p == NULL:
		raise ValueError(
		"pileup buffer out of sync - most likely use of iterator "
		"outside loop")

		if pileup_base_qual_skip(p, self.min_base_quality):
		continue
		result.append(p.b.core.qual)
		@@ -3097,12 +3137,19 @@ cdef class PileupColumn:

		list: a list of read positions
		"""
		if self.plp == NULL or self.plp[0] == NULL:
		raise ValueError("PileupColumn accessed after iterator finished")

		cdef uint32_t x = 0
		cdef bam_pileup1_t * p = NULL
		result = []
		for x from 0 <= x < self.n_pu:
		p = &(self.plp[0][x])
		if p == NULL:
		raise ValueError(
		"pileup buffer out of sync - most likely use of iterator "
		"outside loop")

		if pileup_base_qual_skip(p, self.min_base_quality):
		continue
		result.append(p.qpos)
		@@ -3116,11 +3163,19 @@ cdef class PileupColumn:

		list: a list of query names at pileup column position.
		"""
		if self.plp == NULL or self.plp[0] == NULL:
		raise ValueError("PileupColumn accessed after iterator finished")

		cdef uint32_t x = 0
		cdef bam_pileup1_t * p = NULL
		result = []
		for x from 0 <= x < self.n_pu:
		p = &(self.plp[0][x])
		if p == NULL:
		raise ValueError(
		"pileup buffer out of sync - most likely use of iterator "
		"outside loop")

		if pileup_base_qual_skip(p, self.min_base_quality):
		continue
		result.append(charptr_to_str(pysam_bam_get_qname(p.b)))