.travis.yml

@@ -4,6 +4,11 @@ os:
 
 language: c
 
+stages:
+  - test
+  - name: deploy
+    if: tag IS present
+
 env:
   matrix:
     - CONDA_PY=2.7
@@ -12,12 +17,26 @@ env:
   global:
     - PYSAM_LINKING_TEST=1
     - TWINE_USERNAME=grepall
-    - secure: 'OcwwP8/o21+SGW0UVAnnCQwllhGSCq2HJzpI9EhX3kh6J9RTkyx/+drkg45bx1Z5u8zymuAFappEYzlpzqZE886XezkjOYGVa/u+Coqr1oT/BEJHFCkCA4o26yESp7Zy8aNj/juhB7Rfa77pIDXBayqTzbALz/AURMtZapasB18='
+    - secure: bTbky3Un19NAl62lix8bMLmBv9IGNhFkRXlZH+B253nYub7jwQwPQKum3ct9ea+XHJT5//uM0B8WAF6eyugpNkPQ7+S7SEH5BJuCt30nv6qvGhSO2AffZKeHEDnfW2kqGrivn87TqeomlSBlO742CD/V0wOIUwkTT9tutd+E7FU=
 
-_deploy_common: &deploy_common
-  if: tag IS present
+_cibw_common: &cibw_common
+  addons: {}
   install:
-    - python3 -m pip install cibuildwheel twine
+    - python3 -m pip install cibuildwheel>=1.1.0 twine
+  script:
+    - set -e
+    - cibuildwheel --output-dir dist
+    - twine check dist/*
+    - twine upload --skip-existing dist/*
+
+_cibw_linux: &cibw_linux
+  stage: deploy
+  os: linux
+  language: python
+  python: '3.5'
+  services:
+    - docker
+  <<: *cibw_common
 
 matrix:
   include:
@@ -25,11 +44,6 @@ matrix:
       os: linux
       language: python
       python: '3.5'
-      services:
-        - docker
-      env:
-        - CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && pip install -r requirements.txt"
-        - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
       addons:
         apt:
           packages:
@@ -37,28 +51,36 @@ matrix:
             - g++
             - libcurl4-openssl-dev  # for libcurl support in sdist
             - libssl-dev  # for s3 support in sdist
-      <<: *deploy_common
+      install:
+        - python3 -m pip install Cython twine
       script:
         - set -e
-        - cibuildwheel --output-dir dist
-        - python3 -m pip install Cython
         - python3 setup.py build_ext --inplace
         - python3 setup.py sdist
         - twine check dist/*
         - twine upload --skip-existing dist/*
+    - <<: *cibw_linux
+      env:
+        - CIBW_BUILD="*_x86_64"
+        - CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && python -m pip install -r requirements.txt"
+        - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
+        - CIBW_REPAIR_WHEEL_COMMAND_LINUX='auditwheel repair -L . -w {dest_dir} {wheel}'
+        - CIBW_TEST_COMMAND='python -c "import pysam"'
+    - <<: *cibw_linux
+      env:
+        - CIBW_BUILD="*_i686"
+        - CIBW_BEFORE_BUILD="yum install -y zlib-devel bzip2-devel xz-devel && python -m pip install -r requirements.txt"
+        - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
+        - CIBW_REPAIR_WHEEL_COMMAND_LINUX='auditwheel repair -L . -w {dest_dir} {wheel}'
+        - CIBW_TEST_COMMAND='python -c "import pysam"'
     - stage: deploy
       os: osx
       language: generic
       env:
-        - CIBW_BEFORE_BUILD="pip install -r requirements.txt"
+        - CIBW_BEFORE_BUILD="python -m pip install -r requirements.txt"
         - CIBW_ENVIRONMENT='HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"'
-      addons: {}
-      <<: *deploy_common
-      script:
-        - set -e
-        - cibuildwheel --output-dir dist
-        - twine check dist/*
-        - twine upload --skip-existing dist/*
+        - CIBW_TEST_COMMAND='python -c "import pysam"'
+      <<: *cibw_common
 
 addons:
   apt:

debian/changelog

+python-pysam (0.15.4+ds-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * python-pysam-tests: Multi-Arch: foreign
+  * Try to keep example_no_seq_in_header_null_bytes.bam from being deleted
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 23 Jan 2020 15:00:17 +0100
+
 python-pysam (0.15.3+ds-5) unstable; urgency=medium
 
   [ Chris Lamb ]

debian/control

@@ -52,6 +52,7 @@ Description: interface for the SAM/BAM sequence alignment and mapping format (Py
  This package installs the module for Python 3.
 
 Package: python-pysam-tests
+Multi-Arch: foreign
 Architecture: all
 Depends: ${misc:Depends}
 Enhances: python-pysam

debian/patches/clean_less

+--- python-pysam.orig/tests/pysam_data/Makefile
++++ python-pysam/tests/pysam_data/Makefile
+@@ -87,7 +87,7 @@
+ 	cp ex1.cram $@
+ 
+ clean:
+-	rm -fr *.bam *.bai *.fai *.pileup* *.cram \
++	rm -fr *.bai *.fai *.pileup* *.cram \
+ 	*~ calDepth *.dSYM pysam_*.sam \
+ 	ex2.sam ex2.sam.gz ex1.sam \
+ 	with_md.sam.gz \

debian/patches/series

@@ -4,3 +4,4 @@ hts1.10
 samtools_v1.10_full
 # samtools_v1.10
 bcftools_v1.10_full
+clean_less

doc/release.rst

@@ -2,6 +2,26 @@
 Release notes
 =============
 
+Release 0.15.4
+==============
+
+Bugfix release. Principal reason for release is to update cython
+version in order to fix pip install pysam with python 3.8.
+
+* [#879] Fix add_meta function in libcbcf.pyx, so meta-information
+  lines in header added with this function have double-quoting rules
+  in accordance to rules specified in VCF4.2 and VCF4.3 specifications
+* [#863] Force arg to bytes to support non-ASCII encoding
+* [#875] Bump minimum Cython version
+* [#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
+* [#867] Fix wheel building on TravisCI
+* [#863] Force arg to bytes to support non-ASCII encoding
+* [#799] disambiguate interpretation of bcf_read return code
+* [#841] Fix silent truncation of FASTQ with bad q strings
+* [#846] Prevent segmentation fault on ID, when handling malformed records
+* [#829] Run configure with the correct CC/CFLAGS/LDFLAGS env vars
+
+
 Release 0.15.3
 ==============
 

pysam/bcftools.py

-from utils import PysamDispatcher
+from pysam.utils import PysamDispatcher
 
 BCFTOOLS_DISPATCH = [
     "index",

pysam/libcalignedsegment.pyx

@@ -924,7 +924,8 @@ cdef class AlignedSegment:
     Parameters
     ----------
 
-    header -- :class:`~pysam.AlignmentHeader` object to map numerical
+    header:
+         :class:`~pysam.AlignmentHeader` object to map numerical
          identifiers to chromosome names. If not given, an empty
          header is created.
     '''
@@ -999,6 +1000,10 @@ cdef class AlignedSegment:
         <,=,> to *other*
         '''
 
+        # avoid segfault when other equals None
+        if other is None:
+            return -1
+
         cdef int retval, x
         cdef bam1_t *t
         cdef bam1_t *o
@@ -1088,7 +1093,8 @@ cdef class AlignedSegment:
 
         Parameters
         ----------
-        sam -- :term:`SAM` formatted string
+        sam:
+            :term:`SAM` formatted string
 
         """
         cdef AlignedSegment dest = cls.__new__(cls)
@@ -1110,7 +1116,8 @@ cdef class AlignedSegment:
         Parameters
         ----------
 
-        htsfile -- (deprecated) AlignmentFile object to map numerical
+        htsfile:
+            (deprecated) AlignmentFile object to map numerical
             identifiers to chromosome names. This parameter is present
             for backwards compatibility and ignored.
         """
@@ -1133,7 +1140,8 @@ cdef class AlignedSegment:
 
         Parameters
         ----------
-        sam_dict -- dictionary of alignment values, keys corresponding to output from
+        sam_dict:
+            dictionary of alignment values, keys corresponding to output from
             :meth:`todict()`.
 
         """
@@ -2075,15 +2083,11 @@ cdef class AlignedSegment:
 
         If no cigar string is present, empty arrays will be returned.
 
-        Parameters
-        ----------
-
-        Returns
-        -------
-
-        arrays : two arrays. The first contains the nucleotide counts within
-           each cigar operation, the second contains the number of blocks for
-           each cigar operation.
+        Returns:
+            arrays :
+                two arrays. The first contains the nucleotide counts within
+                each cigar operation, the second contains the number of blocks
+                for each cigar operation.
 
         """
 
@@ -2406,24 +2410,21 @@ cdef class AlignedSegment:
         specification) as well as additional value type 'd' as
         implemented in htslib.
 
-        Parameters
-        ----------
+        Parameters:
 
             tag :
                 data tag.
 
             with_value_type : Optional[bool]
-            if set to True, the return value is a tuple of (tag value, type code).
-            (default False)
+                if set to True, the return value is a tuple of (tag value, type
+                code). (default False)
 
-        Returns
-        -------
+        Returns:
 
             A python object with the value of the `tag`. The type of the
             object depends on the data type in the data record.
 
-        Raises
-        ------
+        Raises:
 
             KeyError
                 If `tag` is not present, a KeyError is raised.

pysam/libcalignmentfile.pyx

@@ -1705,15 +1705,13 @@ cdef class AlignmentFile(HTSFile):
         '''
         write a single :class:`pysam.AlignedSegment` to disk.
 
-        Raises
-        ------
+        Raises:
             ValueError
                 if the writing failed
 
-        Returns
-        -------
-
-        int : the number of bytes written. If the file is closed,
+        Returns:
+            int :
+                the number of bytes written. If the file is closed,
                 this will be 0.
         '''
         if not self.is_open:
@@ -1800,10 +1798,10 @@ cdef class AlignmentFile(HTSFile):
         """return statistics about mapped/unmapped reads per chromosome as
         they are stored in the index.
 
-        Returns
-        -------
-        list : a list of records for each chromosome. Each record has the attributes 'contig',
-               'mapped', 'unmapped' and 'total'.
+        Returns:
+            list :
+                a list of records for each chromosome. Each record has the
+                attributes 'contig', 'mapped', 'unmapped' and 'total'.
         """
 
         self.check_index()

pysam/libcbcf.pyx

@@ -2124,6 +2124,7 @@ cdef class VariantHeader(object):
         if self.ptr.dirty:
             bcf_hdr_sync(self.ptr)
 
+
     def add_meta(self, key, value=None, items=None):
         """Add metadata to this header"""
         if not ((value is not None) ^ (items is not None)):
@@ -2140,11 +2141,16 @@ cdef class VariantHeader(object):
                 hrec.value = strdup(force_bytes(value))
             else:
                 for key, value in items:
+                
+                    quoted = True
+                    if key in set(("ID", "Number", "Type")):
+                      quoted = False
+
                     key = force_bytes(key)
                     bcf_hrec_add_key(hrec, key, <int>len(key))
 
                     value = force_bytes(str(value))
-                    quoted = strpbrk(value, ' ;,"\t<>') != NULL
+
                     bcf_hrec_set_val(hrec, hrec.nkeys-1, value, <int>len(value), quoted)
         except:
             bcf_hrec_destroy(hrec)
@@ -3134,6 +3140,8 @@ cdef class VariantRecord(object):
             raise ValueError('Error unpacking VariantRecord')
         # causes a memory leak https://github.com/pysam-developers/pysam/issues/773
         # return bcf_str_cache_get_charptr(r.d.id) if r.d.id != b'.' else None
+        if (r.d.m_id == 0):
+            raise ValueError('Error extracing ID')
         return charptr_to_str(r.d.id) if r.d.id != b'.' else None
 
     @id.setter
@@ -4080,6 +4088,7 @@ cdef class VariantFile(HTSFile):
 
     def __next__(self):
         cdef int ret
+        cdef int errcode
         cdef bcf1_t *record = bcf_init1()
 
         if not record:
@@ -4093,7 +4102,10 @@ cdef class VariantFile(HTSFile):
             ret = bcf_read1(self.htsfile, self.header.ptr, record)
 
         if ret < 0:
+            errcode = record.errcode
             bcf_destroy1(record)
+            if errcode:
+                raise IOError('unable to parse next record')
             if ret == -1:
                 raise StopIteration
             elif ret == -2:
@@ -4445,3 +4457,4 @@ cdef class VariantFile(HTSFile):
         # potentially unnecessary optimization that also sets max_unpack
         if not include_samples:
             self.drop_samples = True
+

pysam/libcfaidx.pyx

@@ -646,8 +646,14 @@ cdef class FastxFile:
             if self.persist:
                 return FastxRecord(proxy=makeFastqProxy(self.entry))
             return makeFastqProxy(self.entry)
-        else:
+        elif (l == -1):
             raise StopIteration
+        elif (l == -2):
+            raise ValueError('truncated quality string in {0}'
+                             .format(self._filename))
+        else:
+            raise ValueError('unknown problem parsing {0}'
+                             .format(self._filename))
 
 # Compatibility Layer for pysam 0.8.1
 cdef class FastqFile(FastxFile):

pysam/libchtslib.pyx

@@ -617,7 +617,8 @@ cdef class HTSFile(object):
         Returns
         -------
 
-        tuple : a tuple of `flag`, :term:`tid`, `start` and
+        tuple :
+            a tuple of `flag`, :term:`tid`, `start` and
             `stop`. The flag indicates whether no coordinates were
             supplied and the genomic region is the complete genomic space.
 

pysam/libcutils.pyx

@@ -284,7 +284,7 @@ def _pysam_dispatch(collection,
             if skip_next:
                 skip_next = False
                 continue
-            if arg in SIMPLE_FLAGS or (len(arg) > 2 and arg.startswith('-@')):
+            if arg in SIMPLE_FLAGS or (len(arg) > 2 and force_bytes(arg).startswith(b'-@')):
                 continue
             if arg in ARGUMENTS:
                 skip_next = True

pysam/samtools.py

-from utils import PysamDispatcher
+from pysam.utils import PysamDispatcher
 
 # samtools command line options to export in python
 #

pysam/version.py

 # pysam versioning information
-__version__ = "0.15.3"
+__version__ = "0.15.4"
 
 # TODO: upgrade number
 __samtools_version__ = "1.9"

requirements.txt

-cython>=0.24.1
+cython>=0.29.12

setup.py

@@ -29,7 +29,7 @@ import subprocess
 import sys
 import sysconfig
 from contextlib import contextmanager
-from setuptools import Extension, setup
+from setuptools import setup
 from cy_build import CyExtension as Extension, cy_build_ext as build_ext
 try:
     import cython
@@ -443,7 +443,7 @@ metadata = {
     'classifiers': [_f for _f in classifiers.split("\n") if _f],
     'url': "https://github.com/pysam-developers/pysam",
     'packages': package_list,
-    'requires': ['cython (>=0.21)'],
+    'requires': ['cython (>=0.29.12)'],
     'ext_modules': [Extension(**opts) for opts in modules],
     'cmdclass': cmdclass,
     'package_dir': package_dirs,

tests/AlignedSegment_test.py

@@ -78,6 +78,12 @@ class TestAlignedSegment(ReadTest):
     def testCompare(self):
         '''check comparison functions.'''
         a = self.build_read()
+        b = None
+
+        self.assertFalse(a is b)
+        self.assertFalse(a == b)
+        self.assertEqual(-1, a.compare(b))
+
         b = self.build_read()
 
         self.assertEqual(0, a.compare(b))