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<h3>
Saira Hussain pushed to branch master
at <a href="https://salsa.debian.org/med-team/cdbfasta">Debian Med / cdbfasta</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cdbfasta/commit/39d0e6d7f4a24add155d10d10db831bd918bc8df">39d0e6d7</a></strong>
<div>
<span>by Saira Hussain</span>
<i>at 2019-07-31T14:20:10Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Final unit tests
</pre>
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<h4>1 changed file:</h4>
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<a href="#b8880ead45e8d099a1552defb95ea70479f1572e">
debian/tests/run-unit-tests
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<h4>Changes:</h4>
<li id="b8880ead45e8d099a1552defb95ea70479f1572e">
<a href="https://salsa.debian.org/med-team/cdbfasta/commit/39d0e6d7f4a24add155d10d10db831bd918bc8df#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</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">@@ -20,16 +20,13 @@ gunzip -r *</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></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 class="c" style="color: #998; font-style: italic;"># Create the index file for a multi-FASTA</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell">cdbfasta </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">cdbfasta <span class="idiff left right">ebola.fasta</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Pull records based on the index file</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell">cdbyank</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Retrieve records from the database file</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell">cdbyank <span class="nt" style="color: #000080;">-a</span> <span class="s1" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">cdbyank <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"Cote_d'Ivoire_ebolavirus,_complete_genome"</span> ebola.fasta.cidx</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Retrieve specific sequence ranges</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell">cdbyank <span class="nt" style="color: #000080;">-a</span> <span class="s1" style="color: #d14;"><span class="idiff left">''</span></span><span class="idiff right"> <right_coo> <left_coo></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">cdbyank <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;"><span class="idiff left">"Cote_d'Ivoire_ebolavirus,_complete_genome 32 112"</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-R</span></span><span class="idiff right"> ebola.fasta.cidx</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test the compression</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">cdbfasta ebola.fasta <span class="nt" style="color: #000080;">-z</span> ebola.cdbz</span></pre>
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