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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqsero">Debian Med / seqsero</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero/-/commit/68d033a8729b776f27e09e2dd34b316c98453832">68d033a8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-03-10T17:52:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">The output seems to contain CPU time and a few other params which might lead to problems on other arches hence avoid checksum comparision
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero/-/commit/ca5367dca895b3f0905a156ec8fe04916f361148">ca5367dc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-03-10T17:53:13+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor nitpick
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero/-/commit/a7f497203393b745461b597bfc627596c82973f5">a7f49720</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-03-10T17:57:40+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/seqsero/-/compare/c5585ac2f573396a4b20d303980e2e44bbb4a83b...a7f497203393b745461b597bfc627596c82973f5#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</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">@@ -7,7 +7,7 @@ This package can be tested by running the provided test:</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="php"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">confirm</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">integrity</span><span class="mf" style="color: #099;">.</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">testing</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">testing</span></span>
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<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC11" 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="LC12" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Files</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Source</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">https</span><span class="o" style="font-weight: 600;">://</span><span class="n" style="color: #333;">www</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">ncbi</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">nlm</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">nih</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">gov</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sra</span><span class="o" style="font-weight: 600;">/</span><span class="no" style="color: #008080;">SRX839168</span></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seqsero/-/compare/c5585ac2f573396a4b20d303980e2e44bbb4a83b...a7f497203393b745461b597bfc627596c82973f5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">seqsero (1.0.1+dfsg-<span class="idiff left right">2ubuntu1) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seqsero (1.0.1+dfsg-<span class="idiff left right">3) unstable</span>; 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"> * Team Upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * Add test depends on current package, cleaup debug statements</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add test depends on current package,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> cleanup test debug statements</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> [ Shruti Sridhar ]</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * Update 2to3 patch</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * Add autopkgtest. Closes #970598</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> * <span class="idiff left right">Add doc</span>s</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Update 2to3 patch<span class="idiff left right"> (Closes: #984854)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Add autopkgtest. <span class="idiff left">(</span>Closes<span class="idiff">:</span> #970598<span class="idiff right">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * <span class="idiff left right">Both the above changes are meant as targeted fixe</span>s</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> -- Shruti Sridhar <shruti.sridhar99@gmail.com> Sun, 07 Mar 2021 23:47:46 +0530</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/seqsero/-/compare/c5585ac2f573396a4b20d303980e2e44bbb4a83b...a7f497203393b745461b597bfc627596c82973f5#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -13,11 +13,9 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test for checking functionality"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell">seqsero <span class="nt" style="color: #000080;">-m</span> 3 <span class="nt" style="color: #000080;">-i</span> sra_data.fastq</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="si" style="color: #d14;">$(</span>find <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"Seqsero_result.txt"</span><span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">></span> result</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"d87480d5b8ed2cb5125583b02c8694ed result"</span> <span class="o" style="font-weight: 600;">></span> checksums</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> result <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>result</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span></pre>
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