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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/gasic">Debian Med / gasic</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gasic/-/commit/08e971991d615825981d26f94219118818e8def7">08e97199</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-12T04:50:25+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move examples to another binary: gasic-examples
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#7e2b4f79569267d11fc3969aec602513016a7ec4">
<span class="new-file">
+
debian/gasic-examples.examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#ee60a59f58945b7e3e6245ed84d0b7e6b489b427">
debian/docs
→
debian/gasic.docs
</a>
</li>
<li class="file-stats">
<a href="#23cc934c52baf810abb40759d16ea52c9c4095ea">
debian/examples
→
debian/gasic.examples
</a>
</li>
<li class="file-stats">
<a href="#b483097baf6e832d6dd1913ab0e26c39419f476c">
debian/install
→
debian/gasic.install
</a>
</li>
<li class="file-stats">
<a href="#020df36c1e68d966b45d3de0f28a5c32ae3edabc">
debian/links
→
debian/gasic.links
</a>
</li>
<li class="file-stats">
<a href="#57e27374a4527b86f922835d3617bea6af9c6e6f">
debian/manpages
→
debian/gasic.manpages
</a>
</li>
<li class="file-stats">
<a href="#37a610ea78de18684f7427af7f86a3325ed337e6">
<span class="new-file">
+
debian/log.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/gasic/-/commit/08e971991d615825981d26f94219118818e8def7#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num old old_line" data-linenumber="4" 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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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5" 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="4" 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="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">tests</span> <span class="nx">that</span> <span class="nx">come</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5" 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="5" 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="LC5" class="line" lang="php"><span class="nx">with</span> <span class="nx">gasic</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span> <span class="nx">by</span> <span class="nx">the</span> <span class="nx">following</span> <span class="nx">command</span><span class="o" style="font-weight: 600;">:</span> </span>
</pre>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/gasic/-/commit/08e971991d615825981d26f94219118818e8def7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" 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">@@ -38,3 +38,29 @@ Description: genome abundance similarity correction</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> method to correct read alignment results for the ambiguities imposed by</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> similarities of genomes. It has superior performance over existing</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> methods.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="plaintext">Package: gasic-examples</span>
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<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> python3-scipy,</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> python3-numpy,</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> python3-biopython,</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> python3-pysam,</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> python3-matplotlib,</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> bowtie,</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> bowtie2,</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> bwa,</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> seqan-apps,</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> gasic</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Description: genome abundance similarity correction</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> One goal of sequencing based metagenomic analysis is the quantitative</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> taxonomic assessment of microbial community compositions. However, the</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> majority of approaches either quantify at low resolution (e.g. at phylum</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> level) or have severe problems discerning highly similar species. Yet,</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> accurate quantification on species level is desirable in applications</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> such as metagenomic diagnostics or community comparison. GASiC is a</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> method to correct read alignment results for the ambiguities imposed by</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> similarities of genomes. It has superior performance over existing</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> methods.</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> This packages includes some examples that can be used for testing gasic.</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/commit/08e971991d615825981d26f94219118818e8def7#7e2b4f79569267d11fc3969aec602513016a7ec4"><strong>debian/gasic-examples.examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">doc/example_script.py</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/README.example</span></pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/commit/08e971991d615825981d26f94219118818e8def7#b483097baf6e832d6dd1913ab0e26c39419f476c"><strong>debian/install</strong>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usage: autopkgtest [options] [testbinary ...] testsrc -- virt-server [options]</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">autopkgtest: error: . is not a valid test package</span></pre>
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<a href="https://salsa.debian.org/med-team/gasic/-/commit/08e971991d615825981d26f94219118818e8def7#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>gasic</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>gasic<span class="idiff left right">-examples</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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