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<h3>
Shruti Sridhar pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqsero">Debian Med / seqsero</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero/-/commit/6092d93d781a2179a6758783fb6a8c0ec6ebf023">6092d93d</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-03-07T23:45:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update 2to3 patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero/-/commit/368095b189b628d15a55f408f97434ce329476cc">368095b1</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-03-07T23:45:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero/-/commit/f4411d9c92414bb02fd1479b6113ebb5a14537bf">f4411d9c</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-03-07T23:45:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero/-/commit/c5585ac2f573396a4b20d303980e2e44bbb4a83b">c5585ac2</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2021-03-07T23:50:19+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#014fe2bf54762f9c8311e6d5a73aa023f159c287">
<span class="new-file">
+
debian/tests/data/sra_data.fastq
</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/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" 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;">how</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span><span class="mf" style="color: #099;">.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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">
2
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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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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" 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">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">This</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="new_line diff-line-num new" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">unit</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<td class="new_line diff-line-num new" data-linenumber="8" 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">
8
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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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<td class="new_line diff-line-num new" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="10" 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">
10
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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>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="11" 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">
11
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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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<td class="new_line diff-line-num new" data-linenumber="13" 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="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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<pre style="margin: 0;">+<span id="LC14" class="line" lang="php"></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b#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-2ubuntu1) 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"> [ 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="LC6" 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"> * Add docs</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" 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="LC13" class="line" lang="plaintext">seqsero (1.0.1+dfsg-2) unstable; urgency=medium</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"> * Use 2to3 to port from Python2 to Python3</span>
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<a href="https://salsa.debian.org/med-team/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">User_manual.pdf</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</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">@@ -20,8 +20,9 @@ Last-Update: Wed, 11 Dec 2019 16:37:38 +0100</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(dataset[0])</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> os.system("cp "+dataset[0]+" "+make_dir)</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> os.chdir(make_dir)</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="idiff left right"> </span> os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1")</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span> os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1")</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n\n\nResult:\n"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.system("python3 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1")</span></span>
</pre>
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25
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\n\nResult:\n")</span></span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> os.system("cat Seqsero_result.txt")</span>
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27
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> os.system("rm "+dataset[0].split("/")[-1])</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" 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="32" 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">@@ -31,23 +32,26 @@ Last-Update: Wed, 11 Dec 2019 16:37:38 +0100</td>
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31
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> fnameB=dataset[1].split("/")[-1]</span>
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32
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> os.chdir(make_dir)</span>
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33
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "check fastq id and make them in accordance with each other...please wait..."</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("check fastq id and make them in accordance with each other...please wait...")</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2")</span>
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<td class="new_line diff-line-num new" data-linenumber="35" 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">
35
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2")</span></span>
</pre>
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36
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n\n\nResult:\n"</span></span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("check fastq id and make them in accordance with each other...please wait...")</span></span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.system("python3 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2")</span></span>
</pre>
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37
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\n\nResult:\n")</span></span>
</pre>
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38
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> os.system("cat Seqsero_result.txt")</span>
</pre>
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39
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> elif mode_choice=="3":</span>
</pre>
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40
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> os.system("cp "+dataset[0]+" "+make_dir)</span>
</pre>
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41
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> os.chdir(make_dir)</span>
</pre>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="idiff left right"> </span> os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3")</span>
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<td class="new_line diff-line-num new" data-linenumber="44" 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">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span> os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3")</span></span>
</pre>
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43
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<td class="new_line diff-line-num" data-linenumber="45" 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">
45
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n\n\nResult:\n"</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="46" 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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.system("python3 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3")</span></span>
</pre>
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44
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<td class="new_line diff-line-num" data-linenumber="47" 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">
47
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\n\nResult:\n")</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="45" 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">
45
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48
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> os.system("cat Seqsero_result.txt")</span>
</pre>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> elif mode_choice=="4":</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> os.system("cp "+dataset[0]+" "+make_dir)</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> os.chdir(make_dir)</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="idiff left right"> </span> os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span> os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n\n\nResult:\n"</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.system("python3 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n\n\nResult:\n")</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> os.system("cat Seqsero_result.txt")</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b#014fe2bf54762f9c8311e6d5a73aa023f159c287"><strong>debian/tests/data/sra_data.fastq</strong></a>
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<a href="https://salsa.debian.org/med-team/seqsero/-/compare/7471ca9cebf9cde0743773efc5ebf28680e69088...c5585ac2f573396a4b20d303980e2e44bbb4a83b#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">@@ -12,3 +12,12 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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14
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">seqsero <span class="nt" style="color: #000080;">-m</span> 3 <span class="nt" style="color: #000080;">-i</span> sra_data.fastq</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="si" style="color: #d14;">$(</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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18
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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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19
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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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