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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:
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<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/7243a9975f401cd82685aa07d7994c4887c0bdb9">7243a997</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-12-13T07:23:34Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add TODO about spdlog code copy
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<strong><a href="https://salsa.debian.org/med-team/rapmap/commit/203ed6e583851f1eda3ad537d70dba73e4a81bde">203ed6e5</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-12-13T09:13:39Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">More missing headers for salmon
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<h4>3 changed files:</h4>
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+
debian/TODO
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debian/changelog
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debian/rapmap-dev.install
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/rapmap/compare/f50b9d72962e0ccad8e35d0942890cfd1ad65015...203ed6e583851f1eda3ad537d70dba73e4a81bde#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Replace code copy of spdlog by Debian packaged version once either</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">upstream might have switched (see</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> https://github.com/COMBINE-lab/RapMap/issues/44</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">) or we can develop a patch to adapt RapMap code to Debian spdlog.</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/rapmap/compare/f50b9d72962e0ccad8e35d0942890cfd1ad65015...203ed6e583851f1eda3ad537d70dba73e4a81bde#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rapmap (0.12.0+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"> * Add further header files to rapmap-dev since these are used in salmon</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"> -- Andreas Tille <tille@debian.org> Wed, 12 Dec 2018 23:15:17 +0100</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">rapmap (0.12.0+dfsg-1) unstable; urgency=medium</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"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/rapmap/compare/f50b9d72962e0ccad8e35d0942890cfd1ad65015...203ed6e583851f1eda3ad537d70dba73e4a81bde#10e35076ec71b7a6ed006073c4d35a130f148ae3"><strong>debian/rapmap-dev.install</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,16 +6,23 @@ src/RapMapSAIndex.cpp usr/share/rapmap/src</td>
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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="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">bit_</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">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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<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">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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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">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="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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<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">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"><span class="idiff left">rapmap</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">/</span></span><span class="nx">chobo</span></span>
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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</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_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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<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_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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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_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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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">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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<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">Boo</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">FrugalBooMap</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">IndexHeader</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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22
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<pre style="margin: 0;"> <span id="LC22" 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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">RapMapConfig</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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24
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<pre style="margin: 0;"> <span id="LC24" 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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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="php"><span class="k" style="font-weight: 600;">include</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">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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26
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<pre style="margin: 0;"> <span id="LC26" 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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27
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<pre style="margin: 0;"> <span id="LC27" 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>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span><span class="o" style="font-weight: 600;">/</span><span class="nx">SpinLock</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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