.travis.yml

@@ -3,7 +3,6 @@ os:
   - osx
 
 language: c
-sudo: false
 
 env:
   matrix:

MANIFEST.in

@@ -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

@@ -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
 ==============
 

debian/changelog

+python-pysam (0.15.2+ds-1) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.3.0, no changes needed
+  * added Py2 and Py3 versions of ${python:Provides}
+  * Fix lintian found spelling typos.
+  * debian/tests/control.autodep8 → debian/tests/control.
+  * remove errant log.txt from the packages.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 16 Jan 2019 01:47:40 -0800
+
 python-pysam (0.15.1+ds-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -22,7 +22,7 @@ Build-Depends: debhelper (>= 11~),
                bcftools (>= 1.9) <!nocheck>,
                python-pytest <!nocheck>,
                python3-pytest <!nocheck>
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
 Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
 Homepage: http://pysam.readthedocs.org/en/latest
@@ -32,6 +32,7 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python:Depends}
+Provides: ${python:Provides}
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface
@@ -44,6 +45,7 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python3:Depends}
+Provides: ${python3:Provides}
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface

debian/patches/series

 skip_test_remote.patch
 skip_test_needing_missing_data.patch
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix spelling typos, courtesy of lintian
+--- python-pysam.orig/bcftools/filter.c
++++ python-pysam/bcftools/filter.c
+@@ -993,7 +993,7 @@
+ }
+ static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+ {
+-    if ( nstack==0 ) error("Error parsing the expresion\n");
++    if ( nstack==0 ) error("Error parsing the expression\n");
+     token_t *tok = stack[nstack - 1];
+     if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
+ 
+--- python-pysam.orig/bcftools/filter.c.pysam.c
++++ python-pysam/bcftools/filter.c.pysam.c
+@@ -995,7 +995,7 @@
+ }
+ static int func_npass(filter_t *flt, bcf1_t *line, token_t *rtok, token_t **stack, int nstack)
+ {
+-    if ( nstack==0 ) error("Error parsing the expresion\n");
++    if ( nstack==0 ) error("Error parsing the expression\n");
+     token_t *tok = stack[nstack - 1];
+     if ( !tok->nsamples ) error("The function %s works with FORMAT fields\n", rtok->tag);
+ 
+--- python-pysam.orig/pysam/libcalignedsegment.pyx
++++ python-pysam/pysam/libcalignedsegment.pyx
+@@ -2244,7 +2244,7 @@
+         *value*.
+ 
+         An existing value of the same *tag* will be overwritten unless
+-        *replace* is set to False. This is usually not recommened as a
++        *replace* is set to False. This is usually not recommended as a
+         tag may only appear once in the optional alignment section.
+ 
+         If *value* is None, the tag will be deleted.
+--- python-pysam.orig/pysam/libcalignmentfile.pyx
++++ python-pysam/pysam/libcalignmentfile.pyx
+@@ -1023,7 +1023,7 @@
+ 
+         See :meth:`~pysam.HTSFile.parse_region` for more information
+         on how genomic regions can be specified. :term:`reference` and
+-        `end` are also accepted for backward compatiblity as synonyms
++        `end` are also accepted for backward compatibility as synonyms
+         for :term:`contig` and `stop`, respectively.
+ 
+         Without a `contig` or `region` all mapped reads in the file
+@@ -1206,7 +1206,7 @@
+         """perform a :term:`pileup` within a :term:`region`. The region is
+         specified by :term:`contig`, `start` and `stop` (using
+         0-based indexing).  :term:`reference` and `end` are also accepted for
+-        backward compatiblity as synonyms for :term:`contig` and `stop`,
++        backward compatibility as synonyms for :term:`contig` and `stop`,
+         respectively.  Alternatively, a samtools 'region' string
+         can be supplied.
+ 
+@@ -1355,7 +1355,7 @@
+ 
+         The region is specified by :term:`contig`, `start` and `stop`.
+         :term:`reference` and `end` are also accepted for backward
+-        compatiblity as synonyms for :term:`contig` and `stop`,
++        compatibility as synonyms for :term:`contig` and `stop`,
+         respectively.  Alternatively, a :term:`samtools` :term:`region`
+         string can be supplied.
+ 
+@@ -1459,7 +1459,7 @@
+ 
+         The region is specified by :term:`contig`, `start` and `stop`.
+         :term:`reference` and `end` are also accepted for backward
+-        compatiblity as synonyms for :term:`contig` and `stop`,
++        compatibility as synonyms for :term:`contig` and `stop`,
+         respectively.  Alternatively, a :term:`samtools` :term:`region`
+         string can be supplied.  The coverage is computed per-base [ACGT].
+ 
+--- python-pysam.orig/pysam/libchtslib.pxd
++++ python-pysam/pysam/libchtslib.pxd
+@@ -2502,7 +2502,7 @@
+     #         2 if the file is a stream and thus unseekable
+     #         1 if the file contains an EOF block
+     #         0 if the file does not contain an EOF block
+-    #        -1 if an error occured whilst reading the file or we could not seek back to where we were
++    #        -1 if an error occurred whilst reading the file or we could not seek back to where we were
+     #
+     #
+     int cram_check_EOF(cram_fd *fd)
+--- python-pysam.orig/pysam/libchtslib.pyx
++++ python-pysam/pysam/libchtslib.pyx
+@@ -587,7 +587,7 @@
+                 rval = hts_opt_apply(self.htsfile, opts)
+                 if rval != 0:
+                     hts_opt_free(opts)
+-                    raise RuntimeError('An error occured while applying the requested format options')
++                    raise RuntimeError('An error occurred while applying the requested format options')
+                 hts_opt_free(opts)
+ 
+     def parse_region(self, contig=None, start=None, stop=None,
+@@ -597,7 +597,7 @@
+         either be specified by :term:`contig`, `start` and
+         `stop`. `start` and `stop` denote 0-based, half-open
+         intervals. :term:`reference` and `end` are also accepted for
+-        backward compatiblity as synonyms for :term:`contig` and
++        backward compatibility as synonyms for :term:`contig` and
+         `stop`, respectively.
+ 
+         Alternatively, a samtools :term:`region` string can be
+--- python-pysam.orig/pysam/libcutils.pyx
++++ python-pysam/pysam/libcutils.pyx
+@@ -179,7 +179,7 @@
+     `end`. `start` and `end` denote 0-based, half-open intervals.
+     
+     :term:`reference` and `end` are also accepted for backward
+-    compatiblity as synonyms for :term:`contig` and `stop`,
++    compatibility as synonyms for :term:`contig` and `stop`,
+     respectively.
+ 
+     Alternatively, a samtools :term:`region` string can be supplied.

debian/rules

@@ -25,6 +25,7 @@ clean: clean-tests
 
 override_dh_install: clean-tests
 	dh_install -Xtest.gtf.gz
+	find debian -name log.txt -delete
 
 ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))
 override_dh_auto_test: pysam_data.all cbcf_data.all

doc/release.rst

@@ -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

@@ -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)))

pysam/libcalignmentfile.pyx

-
 # cython: embedsignature=True
 # cython: profile=True
 ########################################################
@@ -62,6 +61,8 @@ import warnings
 import array
 from libc.errno  cimport errno, EPIPE
 from libc.string cimport strcmp, strpbrk, strerror
+from libc.stdint cimport INT32_MAX
+
 from cpython cimport array as c_array
 from cpython.version cimport PY_MAJOR_VERSION
 
@@ -94,7 +95,8 @@ IndexStats = collections.namedtuple("IndexStats",
 ########################################################
 ## global variables
 # maximum genomic coordinace
-cdef int  MAX_POS = 2 << 29
+# for some reason, using 'int' causes overlflow
+cdef int MAX_POS = (1 << 31) - 1
 
 # valid types for SAM headers
 VALID_HEADER_TYPES = {"HD" : collections.Mapping,
@@ -1314,7 +1316,8 @@ cdef class AlignmentFile(HTSFile):
         an iterator over genomic positions.
 
         """
-        cdef int rtid, rstart, rstop, has_coord
+        cdef int rtid, has_coord
+        cdef int32_t rstart, rstop
         
         if not self.is_open:
             raise ValueError("I/O operation on closed file")
@@ -2054,7 +2057,6 @@ cdef class IteratorRowRegion(IteratorRow):
 
         IteratorRow.__init__(self, samfile,
                              multiple_iterators=multiple_iterators)
-
         with nogil:
             self.iter = sam_itr_queryi(
                 self.index,

pysam/libcbcf.pyx

@@ -111,7 +111,7 @@ __all__ = ['VariantFile',
 ## Constants
 ########################################################################
 
-cdef int   MAX_POS = 2 << 29
+cdef int MAX_POS = (1 << 31) - 1
 cdef tuple VALUE_TYPES = ('Flag', 'Integer', 'Float', 'String')
 cdef tuple METADATA_TYPES = ('FILTER', 'INFO', 'FORMAT', 'CONTIG', 'STRUCTURED', 'GENERIC')
 cdef tuple METADATA_LENGTHS = ('FIXED', 'VARIABLE', 'A', 'G', 'R')

pysam/libcfaidx.pyx

@@ -287,19 +287,20 @@ cdef class FastaFile:
         cdef char *ref
         cdef int rstart, rend
 
-        reference, rstart, rend = parse_region(reference, start, end, region)
+        contig, rstart, rend = parse_region(reference, start, end, region)
 
-        if reference is None:
+        if contig is None:
             raise ValueError("no sequence/region supplied.")
 
         if rstart == rend:
             return ""
 
-        ref = reference
+        contig_b = force_bytes(contig)
+        ref = contig_b
         with nogil:
             length = faidx_seq_len(self.fastafile, ref)
         if length == -1:
-            raise KeyError("sequence '%s' not present" % reference)
+            raise KeyError("sequence '%s' not present" % contig)
         if rstart >= length:
             return ""
 
@@ -315,7 +316,7 @@ cdef class FastaFile:
             if errno:
                 raise IOError(errno, strerror(errno))
             else:
-                raise ValueError("failure when retrieving sequence on '%s'" % reference)
+                raise ValueError("failure when retrieving sequence on '%s'" % contig)
 
         try:
             return charptr_to_str(seq)

pysam/libchtslib.pyx

@@ -9,10 +9,9 @@
 
 from posix.unistd cimport dup
 from libc.errno  cimport errno
+from libc.stdint cimport INT32_MAX
 from cpython cimport PyBytes_FromStringAndSize
-
 from pysam.libchtslib cimport *
-
 from pysam.libcutils cimport force_bytes, force_str, charptr_to_str, charptr_to_str_w_len
 from pysam.libcutils cimport encode_filename, from_string_and_size
 
@@ -41,7 +40,7 @@ DEF SEEK_CUR = 1
 DEF SEEK_END = 2
 
 # maximum genomic coordinace
-cdef int   MAX_POS = 2 << 29
+cdef int MAX_POS = (1 << 31) - 1
 
 cdef tuple FORMAT_CATEGORIES = ('UNKNOWN', 'ALIGNMENTS', 'VARIANTS', 'INDEX', 'REGIONS')
 cdef tuple FORMATS = ('UNKNOWN', 'BINARY_FORMAT', 'TEXT_FORMAT', 'SAM', 'BAM', 'BAI', 'CRAM', 'CRAI',
@@ -630,8 +629,8 @@ cdef class HTSFile(object):
 
         """
         cdef int rtid
-        cdef long long rstart
-        cdef long long rstop
+        cdef int32_t rstart
+        cdef int32_t rstop
 
         if reference is not None:
             if contig is not None:
@@ -644,7 +643,7 @@ cdef class HTSFile(object):
             stop = end
 
         if contig is None and tid is None and region is None:
-            return 0, 0, 0, 0
+            return 0, 0, 0, MAX_POS
 
         rtid = -1
         rstart = 0

pysam/libcutils.pyx

@@ -12,6 +12,7 @@ from cpython cimport PyBytes_Check, PyUnicode_Check
 from cpython cimport array as c_array
 from libc.stdlib cimport calloc, free
 from libc.string cimport strncpy
+from libc.stdint cimport INT32_MAX, int32_t
 from libc.stdio cimport fprintf, stderr, fflush
 from libc.stdio cimport stdout as c_stdout
 from posix.fcntl cimport open as c_open, O_WRONLY
@@ -24,7 +25,7 @@ from libcbcftools cimport bcftools_main, bcftools_set_stdout, bcftools_set_stder
 
 #####################################################################
 # hard-coded constants
-cdef int MAX_POS = 2 << 29
+cdef int MAX_POS = (1 << 31) - 1
 
 #################################################################
 # Utility functions for quality string conversions
@@ -48,7 +49,10 @@ cpdef array_to_qualitystring(c_array.array qualities, int offset=33):
 
     for x from 0 <= x < len(qualities):
         result[x] = qualities[x] + offset
-    return force_str(result.tostring())
+    if IS_PYTHON3:
+        return force_str(result.tobytes())
+    else:
+        return result.tostring()
 
 
 cpdef qualities_to_qualitystring(qualities, int offset=33):
@@ -198,51 +202,58 @@ cpdef parse_region(contig=None,
        for invalid or out of bounds regions.
 
     """
-    cdef long long rstart
-    cdef long long rend
+    cdef int32_t rstart
+    cdef int32_t rstop
 
+    
+    if reference is not None:
         if contig is not None:
-        reference = contig
+           raise ValueError('contig and reference should not both be specified')
+        contig = reference
+
+    if contig is not None and region is not None:
+        raise ValueError('contig/reference and region should not both be specified')
+        
+    if end is not None:
         if stop is not None:
-        end = stop
+            raise ValueError('stop and end should not both be specified')
+        stop = end
+
+    if contig is None and region is None:
+        raise ValueError("neither contig nor region are given")
 
     rstart = 0
-    rend = MAX_POS
-    if start != None:
+    rstop = MAX_POS
+    if start is not None:
         try:
             rstart = start
         except OverflowError:
             raise ValueError('start out of range (%i)' % start)
 
-    if end != None:
+    if stop is not None:
         try:
-            rend = end
+            rstop = stop
         except OverflowError:
-            raise ValueError('end out of range (%i)' % end)
+            raise ValueError('stop out of range (%i)' % stop)
 
     if region:
-        region = force_str(region)
         if ":" in region:
             contig, coord = region.split(":")
             parts = coord.split("-")
             rstart = int(parts[0]) - 1
             if len(parts) >= 1:
-                rend = int(parts[1])
+                rstop = int(parts[1])
         else:
             contig = region
 
-    if not reference:
-        return None, 0, 0
-
+    if rstart > rstop:
+        raise ValueError('invalid coordinates: start (%i) > stop (%i)' % (rstart, rstop))
     if not 0 <= rstart < MAX_POS:
         raise ValueError('start out of range (%i)' % rstart)
-    if not 0 <= rend <= MAX_POS:
-        raise ValueError('end out of range (%i)' % rend)
-    if rstart > rend:
-        raise ValueError(
-            'invalid region: start (%i) > end (%i)' % (rstart, rend))
+    if not 0 <= rstop <= MAX_POS:
+        raise ValueError('stop out of range (%i)' % rstop)
 
-    return force_bytes(reference), rstart, rend
+    return contig, rstart, rstop
 
 
 def _pysam_dispatch(collection,

pysam/version.py

 # pysam versioning information
-__version__ = "0.15.0"
+__version__ = "0.15.2"
 
 # TODO: upgrade number
 __samtools_version__ = "1.9"

tests/AlignedSegment_test.py

@@ -430,6 +430,35 @@ class TestAlignedSegment(ReadTest):
              (6, 27), (7, 28),
              (8, 29), (9, 30)])
 
+    def test_equivalence_matches_only_and_with_seq(self):
+        a = self.build_read()
+        a.query_sequence = "ACGT" * 2
+        a.cigarstring = "4M1D4M"
+        a.set_tag("MD", "4^x4")
+        full = (list(zip(range(0, 4), range(20, 24), "ACGT")) +
+                [(None, 24, "x")] +
+                list(zip(range(4, 8), range(25, 29), "ACGT")))
+        self.assertEqual(
+            a.get_aligned_pairs(matches_only=False, with_seq=True), full)
+
+        self.assertEqual(
+            a.get_aligned_pairs(matches_only=True, with_seq=True),
+            [x for x in full if x[0] is not None and x[1] is not None])
+
+        a = self.build_read()
+        a.query_sequence = "ACGT" * 2
+        a.cigarstring = "4M1N4M"
+        a.set_tag("MD", "8")
+        full = (list(zip(range(0, 4), range(20, 24), "ACGT")) +
+                [(None, 24, None)] +
+                list(zip(range(4, 8), range(25, 29), "ACGT")))
+        self.assertEqual(
+            a.get_aligned_pairs(matches_only=False, with_seq=True), full)
+
+        self.assertEqual(
+            a.get_aligned_pairs(matches_only=True, with_seq=True),
+            [x for x in full if x[0] is not None and x[1] is not None])
+
     def test_get_aligned_pairs_lowercase_md(self):
         a = self.build_read()
         a.query_sequence = "A" * 10

tests/AlignmentFileHeader_test.py

@@ -121,6 +121,7 @@ class TestHeaderConstruction(unittest.TestCase):
         self.compare_headers(header, self.header_without_text)
         self.check_name_mapping(header)
 
+
 class TestHeaderSAM(unittest.TestCase):
     """testing header manipulation"""
 
@@ -287,6 +288,7 @@ class TestHeaderWriteRead(unittest.TestCase):
     def check_read_write(self, flag_write, header):
 
         fn = get_temp_filename()
+        print(fn)
         with pysam.AlignmentFile(
                 fn,
                 flag_write,
@@ -299,8 +301,12 @@ class TestHeaderWriteRead(unittest.TestCase):
         with pysam.AlignmentFile(fn) as inf:
             read_header = inf.header
 
-        os.unlink(fn)
+        # os.unlink(fn)
         self.compare_headers(header, read_header)
+        expected_lengths = dict([(x["SN"], x["LN"]) for x in header["SQ"]])
+        self.assertEqual(expected_lengths,
+                         dict(zip(read_header.references,
+                                  read_header.lengths)))
 
     def test_SAM(self):
         self.check_read_write("wh", self.header)
@@ -310,6 +316,15 @@ class TestHeaderWriteRead(unittest.TestCase):
         
     def test_CRAM(self):
         header = copy.copy(self.header)
+        if "PG" in header:
             # for CRAM, \t needs to be quoted:
             header['PG'][1]['CL'] = re.sub(r"\t", r"\\\\t", header['PG'][1]['CL'])
         self.check_read_write("wc", header)
+
+
+class TestHeaderLargeContigs(TestHeaderWriteRead):
+    """see issue 741"""
+
+    header = {'SQ': [{'LN': 2147483647, 'SN': 'chr1'},
+                     {'LN': 1584, 'SN': 'chr2'}],
+              'HD': {'VN': '1.0'}}

tests/AlignmentFilePileup_test.py

@@ -206,10 +206,19 @@ class TestPileupObjects(unittest.TestCase):
         '''test if exception is raised if pileup col is accessed after
         iterator is exhausted.'''
 
+        max_n = 0
         for pileupcol in self.samfile.pileup():
-            pass
-
-        self.assertRaises(ValueError, getattr, pileupcol, "pileups")
+            if max_n < pileupcol.n:
+                max_col = pileupcol
+                max_n = pileupcol.n
+
+        self.assertRaises(ValueError, getattr, max_col, "pileups")
+        self.assertRaises(ValueError, max_col.get_query_sequences)
+        self.assertRaises(ValueError, max_col.get_num_aligned)
+        self.assertRaises(ValueError, max_col.get_query_qualities)
+        self.assertRaises(ValueError, max_col.get_mapping_qualities)
+        self.assertRaises(ValueError, max_col.get_query_positions)
+        self.assertRaises(ValueError, max_col.get_query_names)
 
 
 class TestIteratorColumnBAM(unittest.TestCase):