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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/scythe">Debian Med / scythe</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/scythe/-/commit/a925ffa453ace0bb636cf7c2c48eaa362d617946">a925ffa4</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-08-14T15:37:10+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enhance tests
</pre>
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<strong><a href="https://salsa.debian.org/med-team/scythe/-/commit/eaa0550de9d5adcf83010653c047ea0544b2b1d9">eaa0550d</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-08-14T15:38:41+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>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/scythe/-/compare/64bcf7ef1ea32e348e7a2e98045b96b1dfff2b18...eaa0550de9d5adcf83010653c047ea0544b2b1d9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">scythe (0.994+git20141017.20d3cff-3) unstable; 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"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * compat version: 13, standards version: 4.5.0</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add "Rules-Requires-Root:no"</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Add hardening options</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"> -- Nilesh Patra <npatra974@gmail.com> Fri, 14 Aug 2020 15:30:00 +0530</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">scythe (0.994+git20141017.20d3cff-2) unstable; urgency=medium</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"> * Team upload.</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/scythe/-/compare/64bcf7ef1ea32e348e7a2e98045b96b1dfff2b18...eaa0550de9d5adcf83010653c047ea0544b2b1d9#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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="26" 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">@@ -26,6 +26,7 @@ do</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test </span><span class="nv" style="color: #008080;">$i</span><span class="s2" style="color: #d14;">"</span> </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing with prior:</span><span class="nv" style="color: #008080;">$prior</span><span class="s2" style="color: #d14;"> and rep:</span><span class="nv" style="color: #008080;">$rep</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"> scythe <span class="nt" style="color: #000080;">-n</span> 0 <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$prior</span> <span class="nt" style="color: #000080;">-a</span> illumina_adapters.fa reads.fastq <span class="o" style="font-weight: 600;">></span> scythe/results/<span class="nv" style="color: #008080;">$contam_rate</span>/trimmed-<span class="nv" style="color: #008080;">$rep</span>-<span class="nv" style="color: #008080;">$prior</span>.fastq 2> /dev/null</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> scythe/results/<span class="nv" style="color: #008080;">$contam_rate</span>/trimmed-<span class="nv" style="color: #008080;">$rep</span>-<span class="nv" style="color: #008080;">$prior</span>.fastq <span class="o" style="font-weight: 600;">]</span> </span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"> <span class="o" style="font-weight: 600;">((</span>i++<span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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