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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>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/b2a5edcbb1f86062a01d6f12356eac9bc74af9af">b2a5edcb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T20:43:20Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add rapmap-dev package to simplify building salmon and avoid code duplication in salmon package source
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#10e35076ec71b7a6ed006073c4d35a130f148ae3">
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+
debian/rapmap-dev.install
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</a>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rapmap/commit/b2a5edcbb1f86062a01d6f12356eac9bc74af9af#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" 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">@@ -9,6 +9,8 @@ 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="LC9" class="line" lang="plaintext"> * Do not exclude spdlog any more as long as it is not ported to</span>
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<td class="diff-line-num old_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">
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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="LC10" class="line" lang="plaintext"> version spdlog 1.2.x</span>
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<td class="diff-line-num 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">
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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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<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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> duplication in salmon package source</span>
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<pre style="margin: 0;"> <span id="LC14" 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 20:47:27 +0100</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/rapmap/commit/b2a5edcbb1f86062a01d6f12356eac9bc74af9af#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">@@ -66,3 +66,23 @@ Description: example data for rapmap - rapid sensitive and accurate DNA read map</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> other tools.</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> This package contains example data to test this program.</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">Package: rapmap-dev</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Description: rapmap - rapid sensitive and accurate DNA read mapping (some headers)</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> RapMap is a testing ground for ideas in quasi-mapping / (lightweight /</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> pseudo) transcriptome alignment. That means that, at this point, it is</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> somewhat experimental. The develop branch will have the latest</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> improvements and additions, but is not guaranteed to be stable between</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> commits. Breaking changes to the master branch will be accompanied by a</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> tag to the version before the breaking change. Currently, RapMap is a</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> stand-alone quasi-mapper that can be used with other tools. It is also</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> being used as part of Sailfish and Salmon. Eventually, the hope is to</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> create and stabilize an API so that it can be used as a library from</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> other tools.</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> .</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> This package contains some headers and C++ source files which are</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> included by package salmon and are provided here in an accessible</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> way to avoid code duplication. Usually there is no reason to install</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> this package except to build the salmon package.</span></pre>
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<li id="10e35076ec71b7a6ed006073c4d35a130f148ae3">
<a href="https://salsa.debian.org/med-team/rapmap/commit/b2a5edcbb1f86062a01d6f12356eac9bc74af9af#10e35076ec71b7a6ed006073c4d35a130f148ae3"><strong>debian/rapmap-dev.install</strong></a>
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1
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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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2
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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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3
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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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4
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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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5
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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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6
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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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7
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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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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"></span>
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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">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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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">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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