.gitignore

@@ -17,6 +17,7 @@ tests/cbcf_data
 tests/tabix_data
 
 samtools/config.h
+bcftools/config.g
 htslib/config.status
 htslib/config.h
 htslib/config.log

NEWS

@@ -5,10 +5,19 @@ http://pysam.readthedocs.io/en/latest/release.html
 Release notes
 =============
 
+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
+
 Release 0.15.0
 ==============
 
-This release wraps htslib/samtools/bcftools version 1.9.0.
+This release wraps htslib (and friends) version 1.9.
 
 * [#673] permit dash in chromosome name of region string
 * [#656] Support `text` when opening a SAM file for writing

bcftools/config.h

-/* empty config.h created by pysam */
-/* conservative compilation options */

debian/changelog

+python-pysam (0.15.1+ds-1) UNRELEASED; urgency=medium
+
+  * New upstream version.
+    - Removes autogenerated config.h - [many thanks!]
+      https://github.com/pysam-developers/pysam/issues/714
+    - Explicit compatibility with Python 3.7
+  * Removed patch skipping test that complained on missing file
+
+ -- Steffen Moeller <moeller@debian.org>  Fri, 14 Sep 2018 10:44:51 +0200
+
 python-pysam (0.15.0.1+ds-2) UNRELEASED; urgency=medium
 
   * Remove ancient fields X-Python*-Version

debian/patches/series

-skip_test_needing_missing_data.patch
 skip_test_remote.patch
+#skip_test_needing_missing_data.patch

debian/patches/skip_test_remote.patch

@@ -2,9 +2,11 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
 Description: Skip tests trying to access remote site
 
---- a/tests/AlignmentFile_test.py
-+++ b/tests/AlignmentFile_test.py
-@@ -1596,6 +1596,7 @@ class TestDoubleFetchCRAMWithReference(T
+Index: python-pysam/tests/AlignmentFile_test.py
+===================================================================
+--- python-pysam.orig/tests/AlignmentFile_test.py
++++ python-pysam/tests/AlignmentFile_test.py
+@@ -1623,6 +1623,7 @@ class TestDoubleFetchCRAMWithReference(T
      reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
  
  
@@ -12,8 +14,10 @@ Description: Skip tests trying to access remote site
  class TestRemoteFileFTP(unittest.TestCase):
  
      '''test remote access.
---- a/tests/tabix_test.py
-+++ b/tests/tabix_test.py
+Index: python-pysam/tests/tabix_test.py
+===================================================================
+--- python-pysam.orig/tests/tabix_test.py
++++ python-pysam/tests/tabix_test.py
 @@ -1039,6 +1039,7 @@ for vcf_file in vcf_files:
      globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
  

debian/rules

@@ -52,7 +52,7 @@ clean-tests: pysam_data.clean cbcf_data.clean
 	#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
 	find . -name "*.bai*" -delete
 	find . -name "*.cram*" -delete
-	find . -name "*.bam" -delete
+	#find . -name "*.bam" -delete # which deletes files tested
 	rm -rf	tests/pysam_test_work \
 		tests/example_htslib.gtf.gz.tbi \
 		tests/log.txt \
@@ -66,4 +66,5 @@ clean-tests: pysam_data.clean cbcf_data.clean
 		tests/pysam_data/ex1.fa.gz \
 		tests/pysam_data/ex1.fa.gz.gzi \
 		tests/pysam_data/ex1_csi.bam.csi
+	rm -rf .pytest_cache/
 

doc/release.rst

@@ -2,6 +2,15 @@
 Release notes
 =============
 
+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
+
 Release 0.15.0
 ==============
 

pysam/libcalignmentfile.pyx

@@ -1713,8 +1713,13 @@ cdef class AlignmentFile(HTSFile):
         if not self.is_open:
             return 0
 
-        cdef int ret
+        if self.header.ptr.n_targets <= read._delegate.core.tid:
+            raise ValueError(
+                "AlignedSegment refers to reference number {} that "
+                "is larger than the number of references ({}) in the header".format(
+                    read._delegate.core.tid, self.header.ptr.n_targets))
         
+        cdef int ret
         with nogil:
             ret = sam_write1(self.htsfile,
                              self.header.ptr,

tests/AlignmentFileHeader_test.py

@@ -121,7 +121,6 @@ class TestHeaderConstruction(unittest.TestCase):
         self.compare_headers(header, self.header_without_text)
         self.check_name_mapping(header)
 
-        
 class TestHeaderSAM(unittest.TestCase):
     """testing header manipulation"""
 

tests/AlignmentFile_test.py

@@ -1259,7 +1259,7 @@ class TestWrongFormat(unittest.TestCase):
                           'rb')
 
 
-class TestRegionParsiong(unittest.TestCase):
+class TestRegionParsing(unittest.TestCase):
 
     def test_dash_in_chr(self):
         with pysam.AlignmentFile(
@@ -1408,6 +1408,29 @@ class TestEmptyHeader(unittest.TestCase):
         self.assertTrue("@SQ" in str(s.header))
 
 
+class TestMismatchingHeader(unittest.TestCase):
+    '''see issue 716.'''
+
+    def testMismatchingHeader(self):
+        # Note: no chr2
+        header = {
+            'SQ': [{'SN': 'chr1', 'LN': 1575}],
+            'PG': [{'ID': 'bwa', 'PN': 'bwa', 'VN': '0.7.15', 'CL': 'bwa mem xx -'}],
+        }
+
+        dest = get_temp_filename("tmp_ex3.bam")
+        with pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex3.bam')) as inf:
+            with pysam.AlignmentFile(dest, mode="wb", header=header) as outf:
+                for read in inf:
+                    if read.reference_name == "chr1":
+                        outf.write(read)
+                    else:
+                        self.assertRaises(ValueError,
+                                          outf.write,
+                                          read)
+        os.unlink(dest)
+
+
 class TestHeaderWithProgramOptions(unittest.TestCase):
 
     '''see issue 39.'''
@@ -1436,7 +1459,7 @@ class TestTruncatedBAM(unittest.TestCase):
                           pysam.AlignmentFile,
                           os.path.join(BAM_DATADIR, 'ex2_truncated.bam'))
 
-    def testTruncatedBam2(self):
+    def testTruncatedBamIterator(self):
         s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, 'ex2_truncated.bam'),
                                 ignore_truncation=True)
 

tests/pysam_data/Makefile

@@ -91,6 +91,7 @@ clean:
 	rm -fr *.bam *.bai *.fai *.pileup* *.cram \
 	*~ calDepth *.dSYM pysam_*.sam \
 	ex2.sam ex2.sam.gz ex1.sam \
+	with_md.sam.gz \
 	*.fq.gz
 
 %.fq.gz: %.fq

tests/samtools_test.py

@@ -266,7 +266,8 @@ class SamtoolsTest(unittest.TestCase):
             # ignore commands that exit or cause other failures
             # TODO: check - if reheader or phase is run in testStatements, sort fails
             # here
-            if command in ("view", "sort", "bam2fq", "flagstat", "reheader", "stats"):
+            if command in ("view", "sort", "bam2fq", "flagstat", "reheader",
+                           "stats", "idxstats"):
                 continue
             mapped_command = self.get_command(statement, map_to_internal=True)
             pysam_method = getattr(self.module, mapped_command)