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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/gatk_old">Debian Med / gatk_old</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gatk_old/-/commit/31a5e4d3a35841ce43c7c9494f4c021cf631b544">31a5e4d3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-25T22:48:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing gradle/ dir with its embedded jar
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gatk_old/-/commit/e782647d44d78f1cc894c4cdee9db1f0f71e08a7">e782647d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-25T22:50:17+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depending on debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gatk_old/-/commit/d92f0be70127bc7b81b16ac5c42e91382a3d6bec">d92f0be7</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-25T22:51:20+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bumping Standards version to 4.5.0 (Rules-Requires-Root field added)
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</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gatk_old/-/commit/a38d62f7898d9cc5667f3cbc00c9a8d8f0f4e2f0">a38d62f7</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-25T22:52:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deleting old Maven patches as gradle is now used
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/gatk_old/-/commit/aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663">aa7a3a38</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-09-25T23:00:02+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switching build system to gradle
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
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−
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<a href="#51a2138b351b7e17b43c90cb21386ce33c2acc71">
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−
debian/patches/only-free-parts.patch
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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/gatk_old/-/compare/70879254fff34de077503462bb64f72f9dae46fb...aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">gatk (4.1.<span class="idiff left right">2.0+dfsg-1) UNRELEASED; urgency=low</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gatk (4.1.<span class="idiff left right">8.1+dfsg-1) UNRELEASED; urgency=medium</span></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"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- <span class="idiff left right">Andreas Tille <tille@debian.org> Thu, 26 Mar 2015 13:20:02 +01</span>00</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- <span class="idiff left right">Pierre Gruet <pgtdebian@free.fr> Fri, 25 Sep 2020 22:56:23 +02</span>00</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/gatk_old/-/compare/70879254fff34de077503462bb64f72f9dae46fb...aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/gatk_old/-/compare/70879254fff34de077503462bb64f72f9dae46fb...aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,15 +2,16 @@ Source: gatk</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC4" 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="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">Build-Depends: debhelper (>= 12~),</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"> javahelper</span>,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org><span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right"> Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">Build-Depends: debhelper-compat (= 13)</span>,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> default-jdk,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right">maven</span>-debian-helper</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3</span>.0</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right">gradle</span>-debian-helper</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/gatk</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/gatk.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://www.broadinstitute.org/gatk/</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: gatk</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Architecture: any</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/gatk_old/-/compare/70879254fff34de077503462bb64f72f9dae46fb...aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -6,6 +6,7 @@ Files-Excluded: *.data</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> .gitignore</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> .gitattributes</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> .dockerignore</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> gradle</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">Files: *</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Copyright: 2012-2014 The Broad Institute</span>
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<li id="51a2138b351b7e17b43c90cb21386ce33c2acc71">
<a href="https://salsa.debian.org/med-team/gatk_old/-/compare/70879254fff34de077503462bb64f72f9dae46fb...aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663#51a2138b351b7e17b43c90cb21386ce33c2acc71"><strong>debian/patches/only-free-parts.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Thu, 26 Mar 2015 13:20:02 +0100</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: When leaving these chunks mh_make fails - so just remove it</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/pom.xml</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;">+++ b/pom.xml</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -777,31 +777,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> </reporting></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"> <profiles></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;">- <!-- Optionally include protected --></span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <profile></span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <id>protected</id></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <activation></span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <file></span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <exists>${basedir}/protected/pom.xml</exists></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;">- </file></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;">- </activation></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;">- <modules></span></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;">- <module>protected</module></span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </modules></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </profile></span></span>
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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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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!-- Optionally include private --></span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <profile></span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <id>private</id></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <activation></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <file></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <exists>${basedir}/private/pom.xml</exists></span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </file></span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </activation></span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <modules></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;">- <module>private</module></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;">- </modules></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;">- </profile></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <!-- Optionally include private ... mh_make stumbles upon this missing directories --></span></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"> <!-- Optionally do not shade/package jars --></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> <!--</span></pre>
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<a href="https://salsa.debian.org/med-team/gatk_old/-/compare/70879254fff34de077503462bb64f72f9dae46fb...aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">only-free-parts.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/gatk_old/-/compare/70879254fff34de077503462bb64f72f9dae46fb...aa7a3a3804e4d4e22a1bad5ec83dfbacabf3e663#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -18,4 +18,4 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">JAVA_HOME=/usr/lib/jvm/default-java</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">%:</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --buildsystem=maven --with javahelper</span></span></pre>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh $@</span></pre>
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