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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pysam">Debian Med / python-pysam</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/09438982e1cf86c0d4b7e8aa4815ad6fad7e0305">09438982</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2019-02-20T09:50:11Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cope with change to Tabix index format
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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debian/patches/test_index_not_compression
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pysam/commit/09438982e1cf86c0d4b7e8aa4815ad6fad7e0305#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pysam (0.15.2+ds-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * For the Tabix tests: test the index contents, not the compression scheme.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #919928, #920250</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 20 Feb 2019 01:34:19 -0800</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">python-pysam (0.15.2+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-pysam/commit/09438982e1cf86c0d4b7e8aa4815ad6fad7e0305#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">skip_test_remote.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">skip_test_needing_missing_data.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">test_index_not_compression</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pysam/commit/09438982e1cf86c0d4b7e8aa4815ad6fad7e0305#366308d6c6847893ce2544097974cd0f50c4b5ac"><strong>debian/patches/test_index_not_compression</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Subject: Test Tabix index contents, not the compression</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Fixes: https://github.com/samtools/htslib/issues/827</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/tests/tabix_test.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/tests/tabix_test.py</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14,8 +14,6 @@</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> import subprocess</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> import glob</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import re</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import copy</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import tempfile</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> from TestUtils import check_url, load_and_convert, TABIX_DATADIR, get_temp_filename</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> IS_PYTHON3 = sys.version_info[0] >= 3</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -64,6 +62,17 @@</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> return found</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+def checkGZBinaryEqual(filename1, filename2):</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ '''return true if the two files are binary equal.'''</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with gzip.open(filename1, "rb") as infile1:</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d1 = infile1.read()</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ with gzip.open(filename2, "rb") as infile2:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ d2 = infile2.read()</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if d1 == d2:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return True</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return False</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> class TestIndexing(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> filename_idx = os.path.join(TABIX_DATADIR, "example.gtf.gz.tbi")</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -77,7 +86,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> '''test indexing via preset.'''</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> pysam.tabix_index(self.tmpfilename, preset="gff")</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(checkBinaryEqual(</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(checkGZBinaryEqual(</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> self.tmpfilename + ".tbi", self.filename_idx))</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> def test_indexing_to_custom_location_works(self):</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -86,7 +95,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> index_path = get_temp_filename(suffix='custom.tbi')</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> pysam.tabix_index(self.tmpfilename, preset="gff",</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> index=index_path, force=True)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(checkBinaryEqual(index_path, self.filename_idx))</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(checkGZBinaryEqual(index_path, self.filename_idx))</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> os.unlink(index_path)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> def test_indexing_with_explict_columns_works(self):</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -98,7 +107,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> end_col=4,</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> line_skip=0,</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> zerobased=False)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue(checkBinaryEqual(</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertTrue(checkGZBinaryEqual(</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> self.tmpfilename + ".tbi", self.filename_idx))</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> def test_indexing_with_lineskipping_works(self):</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -109,7 +118,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> end_col=4,</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> line_skip=1,</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> zerobased=False)</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertFalse(checkBinaryEqual(</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertFalse(checkGZBinaryEqual(</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> self.tmpfilename + ".tbi", self.filename_idx))</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> def tearDown(self):</span></pre>
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