+python-pysam (0.15.3+ds-1) UNRELEASED; urgency=medium
+
+ * New upstream release.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com> Tue, 06 Aug 2019 19:37:44 +0200
+
python-pysam (0.15.2+ds-2) unstable; urgency=medium
* Team upload.
skip_test_remote.patch
-skip_test_needing_missing_data.patch
spelling
-test_index_not_compression
+++ /dev/null
-Description: do not depend from non-existing data file in make test target
- (There is no such file example_reverse_complement.bam)
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Sat, 17 Feb 2018 15:24:34 +0100
-Forwarded: https://github.com/pysam-developers/pysam/issues/626
-
-Index: python-pysam/tests/AlignmentFile_test.py
-===================================================================
---- python-pysam.orig/tests/AlignmentFile_test.py
-+++ python-pysam/tests/AlignmentFile_test.py
-@@ -1402,11 +1402,6 @@ class TestEmptyHeader(unittest.TestCase)
- 'example_empty_header.bam'))
- self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]})
-
-- def test_bam_without_seq_in_header(self):
-- s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header.bam"))
-- self.assertTrue("SQ" in s.header.to_dict())
-- self.assertTrue("@SQ" in str(s.header))
--
-
- class TestMismatchingHeader(unittest.TestCase):
- '''see issue 716.'''
Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
Description: Skip tests trying to access remote site
-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
+@@ -1631,6 +1631,7 @@
reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
class TestRemoteFileFTP(unittest.TestCase):
'''test remote access.
-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:
+@@ -1014,6 +1014,7 @@
globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
class TestRemoteFileHTTP(unittest.TestCase):
url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
-@@ -1078,25 +1079,28 @@ class TestRemoteFileHTTP(unittest.TestCa
+@@ -1053,25 +1054,28 @@
self.assertEqual(list(self.local_file.header), [])
--- python-pysam.orig/pysam/libcalignedsegment.pyx
+++ python-pysam/pysam/libcalignedsegment.pyx
-@@ -2244,7 +2244,7 @@
+@@ -2238,7 +2238,7 @@
*value*.
An existing value of the same *tag* will be overwritten unless
If *value* is None, the tag will be deleted.
--- python-pysam.orig/pysam/libcalignmentfile.pyx
+++ python-pysam/pysam/libcalignmentfile.pyx
-@@ -1023,7 +1023,7 @@
+@@ -1028,7 +1028,7 @@
See :meth:`~pysam.HTSFile.parse_region` for more information
on how genomic regions can be specified. :term:`reference` and
for :term:`contig` and `stop`, respectively.
Without a `contig` or `region` all mapped reads in the file
-@@ -1206,7 +1206,7 @@
+@@ -1211,7 +1211,7 @@
"""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
respectively. Alternatively, a samtools 'region' string
can be supplied.
-@@ -1355,7 +1355,7 @@
+@@ -1360,7 +1360,7 @@
The region is specified by :term:`contig`, `start` and `stop`.
:term:`reference` and `end` are also accepted for backward
respectively. Alternatively, a :term:`samtools` :term:`region`
string can be supplied.
-@@ -1459,7 +1459,7 @@
+@@ -1464,7 +1464,7 @@
The region is specified by :term:`contig`, `start` and `stop`.
:term:`reference` and `end` are also accepted for backward
--- python-pysam.orig/pysam/libchtslib.pxd
+++ python-pysam/pysam/libchtslib.pxd
-@@ -2502,7 +2502,7 @@
+@@ -2513,7 +2513,7 @@
# 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
+++ /dev/null
-From: Michael R. Crusoe <michael.crusoe@gmail.com>
-Subject: Test Tabix index contents, not the compression
-
-Fixes: https://github.com/samtools/htslib/issues/827
-
---- python-pysam.orig/tests/tabix_test.py
-+++ python-pysam/tests/tabix_test.py
-@@ -14,8 +14,6 @@
- import subprocess
- import glob
- import re
--import copy
--import tempfile
- from TestUtils import check_url, load_and_convert, TABIX_DATADIR, get_temp_filename
-
- IS_PYTHON3 = sys.version_info[0] >= 3
-@@ -64,6 +62,17 @@
- return found
-
-
-+def checkGZBinaryEqual(filename1, filename2):
-+ '''return true if the two files are binary equal.'''
-+ with gzip.open(filename1, "rb") as infile1:
-+ d1 = infile1.read()
-+ with gzip.open(filename2, "rb") as infile2:
-+ d2 = infile2.read()
-+ if d1 == d2:
-+ return True
-+ return False
-+
-+
- class TestIndexing(unittest.TestCase):
- filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
- filename_idx = os.path.join(TABIX_DATADIR, "example.gtf.gz.tbi")
-@@ -77,7 +86,7 @@
- '''test indexing via preset.'''
-
- pysam.tabix_index(self.tmpfilename, preset="gff")
-- self.assertTrue(checkBinaryEqual(
-+ self.assertTrue(checkGZBinaryEqual(
- self.tmpfilename + ".tbi", self.filename_idx))
-
- def test_indexing_to_custom_location_works(self):
-@@ -86,7 +95,7 @@
- index_path = get_temp_filename(suffix='custom.tbi')
- pysam.tabix_index(self.tmpfilename, preset="gff",
- index=index_path, force=True)
-- self.assertTrue(checkBinaryEqual(index_path, self.filename_idx))
-+ self.assertTrue(checkGZBinaryEqual(index_path, self.filename_idx))
- os.unlink(index_path)
-
- def test_indexing_with_explict_columns_works(self):
-@@ -98,7 +107,7 @@
- end_col=4,
- line_skip=0,
- zerobased=False)
-- self.assertTrue(checkBinaryEqual(
-+ self.assertTrue(checkGZBinaryEqual(
- self.tmpfilename + ".tbi", self.filename_idx))
-
- def test_indexing_with_lineskipping_works(self):
-@@ -109,7 +118,7 @@
- end_col=4,
- line_skip=1,
- zerobased=False)
-- self.assertFalse(checkBinaryEqual(
-+ self.assertFalse(checkGZBinaryEqual(
- self.tmpfilename + ".tbi", self.filename_idx))
-
- def tearDown(self):
projects / python-pysam.git / commitdiff