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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bowtie">Debian Med / bowtie</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/3311d3cc3e52449cc1d5bbe81db05623ae85447f">3311d3cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T17:46:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watch file to not detect beta versions
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/6196bd2364ab80057f2c0eaaae617cd9cee4294b">6196bd23</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T17:46:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/bd4f1ea07d5e6673df4d80b5211924badc2c1342">bd4f1ea0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T17:46:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.1.4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/564521e646023d439dfc0a82656def8096cf9631">564521e6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T17:55:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/99c9779e44148635e72493d4c43c1509e31161bb">99c9779e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T17:59:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/commit/302a14039001b7ee3a98b509ab374ebc11924ca5">302a1403</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T18:08:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#79da3ac3a45ac3bdc06beffa23bbbb7cf4bd5d0a">
debian/patches/gcc-64bit.patch
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/bowtie/compare/c67e17f9d522165bbb4caa178b058b46bfef547c...302a14039001b7ee3a98b509ab374ebc11924ca5#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" 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="diff-line-num unfold js-unfold new_line" data-linenumber="65" 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">@@ -65,7 +65,7 @@ From: Scott Christley <schristley@mac.com>:</td>
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<td class="diff-line-num old_line" data-linenumber="65" 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="LC65" class="line" lang="plaintext"> From looking at the bowtie output you provided, the content is the same.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="66" 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="66" 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="LC66" class="line" lang="plaintext"> The sequence id names, position and mismatches are identical in both</span>
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<td class="diff-line-num old_line" data-linenumber="67" 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="67" 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="LC67" class="line" lang="plaintext"> outputs, the only difference is the order. That may not even be</span>
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<td class="diff-line-num old old_line" data-linenumber="68" 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="LC68" class="line" lang="plaintext"> bowtie's fault, it may be using some system or other library which</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="69" 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="68" 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="LC68" class="line" lang="plaintext"> bowtie's fault, it may be using some system<span class="idiff left right">s</span> or other library which</span>
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<td class="diff-line-num old_line" data-linenumber="69" 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="69" 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="LC69" class="line" lang="plaintext"> does sorting slightly differently, and most specifically handling ties</span>
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<td class="diff-line-num old_line" data-linenumber="70" 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="LC70" class="line" lang="plaintext"> differently.</span>
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<td class="diff-line-num old_line" data-linenumber="71" 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="LC71" class="line" lang="plaintext"></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bowtie/compare/c67e17f9d522165bbb4caa178b058b46bfef547c...302a14039001b7ee3a98b509ab374ebc11924ca5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bowtie (1.2.2+dfsg-3) unstable; 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"> * Fix watch file to not detect beta versions</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.1.4</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"> -- Andreas Tille <tille@debian.org> Wed, 23 May 2018 17:59:29 +0200</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">bowtie (1.2.2+dfsg-2) 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"> * Update d/tests/run-unit-test</span>
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<a href="https://salsa.debian.org/med-team/bowtie/compare/c67e17f9d522165bbb4caa178b058b46bfef547c...302a14039001b7ee3a98b509ab374ebc11924ca5#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">@@ -13,9 +13,9 @@ Build-Depends: debhelper (>= 11),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> seqan-dev (>= 1.4),</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/bowtie.git</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/bowtie.git</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.1.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/bowtie</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/bowtie.git</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: http://bowtie-bio.sourceforge.net/</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Package: bowtie</span>
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<a href="https://salsa.debian.org/med-team/bowtie/compare/c67e17f9d522165bbb4caa178b058b46bfef547c...302a14039001b7ee3a98b509ab374ebc11924ca5#79da3ac3a45ac3bdc06beffa23bbbb7cf4bd5d0a"><strong>debian/patches/gcc-64bit.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">@@ -6,7 +6,7 @@ Description: Use gcc to determine if an arch is 64-bit</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> on x86_64). This is common on the mips buildds.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> Therefore ask GCC if this architecture is 64-bit. Using __LP64__ is the easiest</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> method, but is not portable and probably only works with GCC and Clang</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> unfortunatly.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> unfortunat<span class="idiff left right">e</span>ly.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff">Author: James Cowgill <jcowgill@debian.org></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff">---</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span>
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<a href="https://salsa.debian.org/med-team/bowtie/compare/c67e17f9d522165bbb4caa178b058b46bfef547c...302a14039001b7ee3a98b509ab374ebc11924ca5#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</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">opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/BenLangmead/bowtie/releases .*/archive/v<span class="idiff left right">@ANY_VERSION@</span>@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/BenLangmead/bowtie/releases .*/archive/v<span class="idiff left right">(\d[-.\d]+)</span>@ARCHIVE_EXT@</span></pre>
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