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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pysam">Debian Med / python-pysam</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/ccef4ca24c6f77a419a473ea44a9a5d074d4efe8">ccef4ca2</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-09-14T11:32:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjustments
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/9099420a0f56bbb65bc960f829831fa4b79ea45f">9099420a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-09-14T11:32:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of salsa.debian.org:med-team/python-pysam
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/92ad28b6839da6eb8de3ca5e76b101ea32bb7345">92ad28b6</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-09-14T12:32:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of salsa.debian.org:med-team/python-pysam
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/8f48c352c71e994a0cc5238886c44b818524fb0a">8f48c352</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-09-14T13:04:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Giving up for the moment - something deletes this file
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-pysam/commit/75779a9f8054ec45e17dfdfb637e311333ad9036">75779a9f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-09-14T20:47:07Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Team upload - avoiding lintian warning
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#becddaf205c06c0a5b64707bb63a0c203baff48a">
debian/patches/skip_test_needing_missing_data.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/07dd508c5a5c866fbe438fe546c2178ae7762abe...75779a9f8054ec45e17dfdfb637e311333ad9036#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-pysam (0.15.1+ds-1) UNRELEASED; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pysam (0.15.1+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * New upstream version.</span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> - Removes autogenerated config.h - [many thanks!]</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/07dd508c5a5c866fbe438fe546c2178ae7762abe...75779a9f8054ec45e17dfdfb637e311333ad9036#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"><span class="idiff left right">#</span>skip_test_needing_missing_data.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">skip_test_needing_missing_data.patch</span></pre>
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<li id="becddaf205c06c0a5b64707bb63a0c203baff48a">
<a href="https://salsa.debian.org/med-team/python-pysam/compare/07dd508c5a5c866fbe438fe546c2178ae7762abe...75779a9f8054ec45e17dfdfb637e311333ad9036#becddaf205c06c0a5b64707bb63a0c203baff48a"><strong>debian/patches/skip_test_needing_missing_data.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Index: python-pysam/tests/AlignmentFile_test.py</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-pysam.orig/tests/AlignmentFile_test.py</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-pysam/tests/AlignmentFile_test.py</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -140<span class="idiff left right">3,12 +1403,7</span> @@ class TestEmptyHeader(unittest.TestCase)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -140<span class="idiff left right">2,11 +1402,6</span> @@ class TestEmptyHeader(unittest.TestCase)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> 'example_empty_header.bam'))</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> self.assertEqual(s.header.to_dict(), {'SQ': [{'LN': 1000, 'SN': 'chr1'}]})</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,8 +16,7 @@ Index: python-pysam/tests/AlignmentFile_test.py</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "example_no_seq_in_header.bam"))</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue("SQ" in s.header.to_dict())</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertTrue("@SQ" in str(s.header))</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> class TestHeaderWithProgramOptions(unittest.TestCase):</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> '''see issue 39.'''</span></pre>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> class TestMismatchingHeader(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> '''see issue 716.'''</span></pre>
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