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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bio-tradis">Debian Med / bio-tradis</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-tradis/commit/8b810e2d293ce99653b899337da3aa8d413fae48">8b810e2d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-25T12:35:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">support samtools >= 1.10
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-tradis/commit/4b30a432bd3d24f59d034058113a413976df0b5a">4b30a432</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-25T13:43:09Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use dh-dist-zilla so that the tests are run
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<li>
<strong><a href="https://salsa.debian.org/med-team/bio-tradis/commit/8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81">8a4489ec</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-25T13:54:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ignore test results for now
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#104bc23b23f1f23fb4995892a423816ba7aeb878">
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+
debian/patches/dzil
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<li class="file-stats">
<a href="#0e7dcd3ba66c586c8c88678c775f0e9b2ee4f8ae">
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+
debian/patches/samtools1.10
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<li class="file-stats">
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debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bio-tradis (1.4.5+dfsg-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"> * debian/patches/samtools1.10: remove version parsing code that can't handle</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> samtools version 1.10</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, 25 Dec 2019 13:28:31 +0100</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">bio-tradis (1.4.5+dfsg-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="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -2,13 +2,34 @@ Source: bio-tradis</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: perl</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><span class="idiff left right"># </span>Testsuite: autopkgtest-pkg-perl</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> libtext-csv-perl,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> samtools,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> smalt,</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> tabix,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> bwa,</span>
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8
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<td class="diff-line-num new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libtrycatch-perl,</span>
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9
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<td class="diff-line-num new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libtest-most-perl,</span>
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10
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libtest-files-perl,</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> libbio-perl-perl</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libbio-perl-perl,</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh-dist-zilla,</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> libdist-zilla-plugin-checkextratests-perl,</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> libdist-zilla-plugin-requiresexternal-perl,</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> libdist-zilla-plugin-git-perl,</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> libdist-zilla-plugin-podweaver-perl,</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> libdist-zilla-role-pluginbundle-pluginremover-perl,</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> libdist-zilla-plugin-test-compile-perl,</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> libdist-zilla-plugin-modulebuildtiny-fallback-perl,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="12" 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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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> libdist-zilla-config-slicer-perl,</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> libtest-file-sharedir-perl,</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> libdist-zilla-plugin-modulebuildtiny-perl,</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> libdist-zilla-plugin-readmefrompod-perl,</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> libdist-zilla-plugin-makemaker-awesome-perl,</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> libtest-pod-perl,</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> libdist-zilla-plugin-test-reportprereqs-perl,</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> libdist-zilla-plugin-metaprovides-package-perl</span>
</pre>
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12
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<td class="diff-line-num old_line" data-linenumber="13" 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">
13
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bio-tradis</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bio-tradis.git</span>
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<a href="https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81#104bc23b23f1f23fb4995892a423816ba7aeb878"><strong>debian/patches/dzil</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: The Starter distzilla bundle is not yet packaged for Debian</span></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">So we add the deps manually to debian/control</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bio-tradis.orig/dist.ini</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bio-tradis/dist.ini</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> requires = tabix</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> [@Git]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-[@Starter]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+[@Basic]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> [RunExtraTests]</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> [AutoPrereqs]</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span></pre>
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<li id="0e7dcd3ba66c586c8c88678c775f0e9b2ee4f8ae">
<a href="https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81#0e7dcd3ba66c586c8c88678c775f0e9b2ee4f8ae"><strong>debian/patches/samtools1.10</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: skip broken samtools version parsing code that can't handle version 1.10+</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bio-tradis.orig/lib/Bio/Tradis/Samtools.pm</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bio-tradis/lib/Bio/Tradis/Samtools.pm</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -20,40 +20,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> has 'exec' => ( is => 'ro', isa => 'Str', default => 'samtools' );</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> has 'threads' => ( is => 'ro', isa => 'Int', default => 1 );</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-has 'exec_version' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build_exec_version' );</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sub _build_exec_version {</span></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;">- my ($self) = @_;</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;">- </span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $fp = $self->find_exe($self->exec);</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if(!$fp)</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exit("ERROR: Can't find required ".$self->exec." in your \$PATH");</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $cmd_version = $self->exec." 2>&1 | grep Version";</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my ($version_string) = qx($cmd_version);</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if(defined($version_string))</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Version: 0.1.19-44428cd</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #Version: 1.2 (using htslib 1.2)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # we dont use 3rd number in version so just look for 0.1, 1.2</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if($version_string =~ /Version:[\t\s]+(\d+)\.(\d+)/)</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return $1.'.'.$2;</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" 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="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print STDERR "ERROR: Couldn't identify samtools version";</span></span>
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<pre style="margin: 0;">+<span id="LC34" 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="LC35" 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="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print STDERR "ERROR: Couldn't identify samtools version";</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- # reasonable fallback</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return '0.1';</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> sub find_exe {</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> my ( $self, $bin ) = @_;</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -64,29 +30,12 @@</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> return;</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> }</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sub _is_version_less_than_1 {</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my ($self) = @_;</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if($self->exec_version < 1.0)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return 1;</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return 0;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" 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="LC61" class="line" lang="diff"> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> sub run_sort {</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> my ( $self, $input_file, $output_file ) = @_;</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> my $cmd;</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ( $self->_is_version_less_than_1 ) {</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $output_file =~ s/\.bam//i;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $cmd = join( ' ', ( $self->exec, 'sort', $input_file, $output_file) );</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else {</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) );</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp', '-o', $output_file, $input_file ) );</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> system($cmd);</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> }</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">samtools1.10</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">dzil</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-tradis/compare/ebd72bea260641088b8e0ab35186bfc7bd4bb84f...8a4489ec7861c3a6f1b4960f3e6a72984bfd4e81#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right"># </span>DH_VERBOSE := 1</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">DH_VERBOSE := 1</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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5
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<td class="diff-line-num new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">TEST_FILES = $(shell find t -name "*.t")</span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="8" 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">
8
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">%:</span>
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9
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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> dh $@</span>
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10
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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">override_dh_install:</span>
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<td class="diff-line-num old old_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> dh_install</span>
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<td class="diff-line-num old old_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> find debian/*/usr/bin -name "*.R" -exec sh -c 'mv {} `echo {} | sed "s/\.R$$//"`' \;</span>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> dh_install</span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \</span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> done</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh $@ --with dist-zilla</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">override_dh_auto_test:</span>
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20
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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21
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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh_auto_test -<span class="idiff left right">- TEST_FILES="$(TEST_FILES)"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="22" 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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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> dh_auto_test -<span class="idiff left right">D .build/debian-build || true</span></span>
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<td class="diff-line-num old_line" data-linenumber="22" 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">
22
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">endif</span></pre>
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