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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mapdamage">Debian Med / mapdamage</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/f2d42c25cc493b3ef3e7dc05014f999150ba1b6b">f2d42c25</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-03T16:36:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure test can be called also from somewhere else than mapdamage dir
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/92d202724506ca4b51833fbf5eaac9603c1dc106">92d20272</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-03T16:45:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix two remaining python instances
</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/2aa3d4df4c0dfa23f6dca110af1999f2b91c0e07...92d202724506ca4b51833fbf5eaac9603c1dc106#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -254,11 +254,14 @@ Last-Update: Tue, 03 Sep 2019 11:02:34 +0200</td>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="diff"> if ((nt_seq == "T" and nt_ref =="C") or (nt_seq == "A" and nt_ref =="G")):</span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/rescale_test.py</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/rescale_test.py</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff"><span class="p">@@ -1,6 +1,<span class="idiff left right">6</span> @@</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="p">@@ -1,6 +1,<span class="idiff left right">9</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="diff"> import unittest</span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="diff"> import optparse</span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import rescale</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import rescale</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import rescale</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except:</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from mapdamage import rescale</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="diff"> import pysam</span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="diff"> import filecmp</span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="409" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -406,9 +409,12 @@ Last-Update: Tue, 03 Sep 2019 11:02:34 +0200</td>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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407
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="diff"> from distutils.core import setup</span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="diff"><span class="p">@@ -16,7 +16,7 @@</span> def setup_version():</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="p">@@ -14,9 +14,9 @@</span> def setup_version():</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> version = subprocess.check_output(("git", "describe", "--always", "--tags", "--dirty"))</span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="diff"> with open(os.path.join("mapdamage", "_version.py"), "w") as handle:</span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="diff"> handle.write("#!/usr/bin/env python\n")</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- handle.write("#!/usr/bin/env python\n")</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ handle.write("#!/usr/bin/python3\n")</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="diff"> handle.write("__version__ = %r\n" % (version.strip(),))</span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- except (subprocess.CalledProcessError, OSError), error:</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ except (subprocess.CalledProcessError, OSError) as error:</span></span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/2aa3d4df4c0dfa23f6dca110af1999f2b91c0e07...92d202724506ca4b51833fbf5eaac9603c1dc106#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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">...</td>
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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">@@ -12,7 +12,7 @@ cd $ADTTMP</td>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/tests/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/ref_T.fa <span class="nb" style="color: #0086b3;">.</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell">python rescale_test.py</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">python<span class="idiff left right">3</span> rescale_test.py</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell">mapDamage <span class="nt" style="color: #000080;">-i</span> rescale_test/pe_test/pe.sam <span class="nt" style="color: #000080;">-r</span> ref_T.fa</span>
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