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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/rapmap">Debian Med / rapmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/54475a3f40395cf8dee5500795148e7703c55c9e">54475a3f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T20:48:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lintian override for script-with-language-extension
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/f9108f8e97e836396e394b5bfbfb3b9a3723e67a">f9108f8e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T21:35:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More header files needed in salmon
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/7d0171bb8c439dfbd1bd6dc19e367fe4024f73a9">7d0171bb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T21:36:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Avoid privacy breach by pointing to pre-fetched copy of the image in question
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/20b415100a2e74e46f2169c35c23051c16dc6403">20b41510</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T22:04:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add even more header files needed by salmon
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/f50b9d72962e0ccad8e35d0942890cfd1ad65015">f50b9d72</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T22:06:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#99969417a0222aa7d30661fbec62bc227127e99e">
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+
debian/imgs/Join_Chat.svg
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<li class="file-stats">
<a href="#03cce9526b9236ae11584cbaa2b92539d969a6a6">
<span class="new-file">
+
debian/patches/avoid_privacy_breach.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#10e35076ec71b7a6ed006073c4d35a130f148ae3">
debian/rapmap-dev.install
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<li class="file-stats">
<a href="#5b33d9c74acd73f884ff22b353ce5c534de21ea7">
debian/rapmap.docs
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<li class="file-stats">
<a href="#a6163eb70bb3152f3e3422bdd0aad6dc66834cc5">
<span class="new-file">
+
debian/rapmap.lintian-overrides
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rapmap/compare/b2a5edcbb1f86062a01d6f12356eac9bc74af9af...f50b9d72962e0ccad8e35d0942890cfd1ad65015#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">rapmap (0.12.0+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
</pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rapmap (0.12.0+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
</pre>
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<td class="diff-line-num old_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">
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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="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" 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="3" 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="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,8 +11,10 @@ rapmap (0.12.0+dfsg-1) UNRELEASED; urgency=medium</td>
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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="LC11" class="line" lang="plaintext"> Closes: #909766</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_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">
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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="LC12" class="line" lang="plaintext"> * Add rapmap-dev package to simplify building salmon and avoid code</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">
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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="LC13" class="line" lang="plaintext"> duplication in salmon package source</span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Lintian override for script-with-language-extension</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> * Avoid privacy breach</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 12 Dec 2018 2<span class="idiff left right">0:47:27</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 12 Dec 2018 2<span class="idiff left right">3:05:04</span> +0100</span>
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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">rapmap (0.5.0+dfsg-3) unstable; urgency=medium</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="LC1" class="line" lang="xml"><span class="nt" style="color: navy;"><svg</span> <span class="na" style="color: teal;">xmlns=</span><span class="s" style="color: #d14;">"http://www.w3.org/2000/svg"</span> <span class="na" style="color: teal;">width=</span><span class="s" style="color: #d14;">"99"</span> <span class="na" style="color: teal;">height=</span><span class="s" style="color: #d14;">"20"</span><span class="nt" style="color: navy;">><linearGradient</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"b"</span> <span class="na" style="color: teal;">x2=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: teal;">y2=</span><span class="s" style="color: #d14;">"100%"</span><span class="nt" style="color: navy;">><stop</span> <span class="na" style="color: teal;">offset=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: 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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Avoid privacy breach by pointing to pre-fetched copy of the image in question</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: Wed, 12 Dec 2018 20:47:27 +0100</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;">--- a/README.md</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;">+++ b/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-[](https://gitter.im/COMBINE-lab/RapMap?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+[](https://gitter.im/COMBINE-lab/RapMap?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # What is RapMap?</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/b2a5edcbb1f86062a01d6f12356eac9bc74af9af...f50b9d72962e0ccad8e35d0942890cfd1ad65015#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use-debian-libs.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use_shared_libs.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">avoid_privacy_breach.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/b2a5edcbb1f86062a01d6f12356eac9bc74af9af...f50b9d72962e0ccad8e35d0942890cfd1ad65015#10e35076ec71b7a6ed006073c4d35a130f148ae3"><strong>debian/rapmap-dev.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bit_array</span><span class="o" style="font-weight: 600;">.</span><span class="nx">c</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">HitManager</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rank9b</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapFileSystem</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapSAIndex</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapSAIndexer</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapUtils</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bit_array</span><span class="o" style="font-weight: 600;">.</span><span class="nx">c</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">HitManager</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rank9b</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapFileSystem</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapSAIndex</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapSAIndexer</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapUtils</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="idiff left right"> </span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">src</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">macros</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rank9b</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Kmer</span><span class="o" style="font-weight: 600;">.</span><span class="nx">hpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapFileSystem</span><span class="o" style="font-weight: 600;">.</span><span class="nx">hpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span></pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">kseq</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">macros</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rank9b</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">chobo</span><span class="o" style="font-weight: 600;">/</span><span class="nx">small_vector</span><span class="o" style="font-weight: 600;">.</span><span class="nx">hpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">chobo</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">spp</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">spp_config</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">spp_stdint</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">spp_traits</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">spp_utils</span><span class="o" style="font-weight: 600;">.</span><span class="nx">h</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">sparsepp</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Kmer</span><span class="o" style="font-weight: 600;">.</span><span class="nx">hpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapFileSystem</span><span class="o" style="font-weight: 600;">.</span><span class="nx">hpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapUtils</span><span class="o" style="font-weight: 600;">.</span><span class="nx">hpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">SparseHashSerializer</span><span class="o" style="font-weight: 600;">.</span><span class="nx">hpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">rapmap</span></span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/b2a5edcbb1f86062a01d6f12356eac9bc74af9af...f50b9d72962e0ccad8e35d0942890cfd1ad65015#5b33d9c74acd73f884ff22b353ce5c534de21ea7"><strong>debian/rapmap.docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/imgs</span></pre>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/b2a5edcbb1f86062a01d6f12356eac9bc74af9af...f50b9d72962e0ccad8e35d0942890cfd1ad65015#a6163eb70bb3152f3e3422bdd0aad6dc66834cc5"><strong>debian/rapmap.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">rapmap: script-with-language-extension usr/bin/RunRapMap.sh</span></pre>
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