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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/wtdbg2">Debian Med / wtdbg2</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/3f0839596fec4271a452d11c13e996aa6b60d7bd">3f083959</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-08-09T21:24:28+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize autopkgtest
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<h4>1 changed file:</h4>
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/3f0839596fec4271a452d11c13e996aa6b60d7bd#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="27" 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="27" 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">@@ -27,9 +27,3 @@ wtpoa-cns -t 16 -i dbg.ctg.lay.gz -fo dbg.raw.fa</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> dbg.raw.fa <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="LC28" 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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<td class="diff-line-num old_line" data-linenumber="29" 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="LC29" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># polish consensus, not necessary if you want to polish the assemblies using other tools</span></span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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="LC31" class="line" lang="shell">minimap2 <span class="nt" style="color: #000080;">-t16</span> <span class="nt" style="color: #000080;">-ax</span> map-pb <span class="nt" style="color: #000080;">-r2k</span> dbg.raw.fa pacbio_filtered.fastq | samtools <span class="nb" style="color: #0086b3;">sort</span> -@4 <span class="o" style="font-weight: 600;">></span>dbg.bam</span>
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<td class="diff-line-num old old_line" data-linenumber="32" 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="LC32" class="line" lang="shell">samtools view <span class="nt" style="color: #000080;">-F0x900</span> dbg.bam | wtpoa-cns <span class="nt" style="color: #000080;">-t</span> 16 <span class="nt" style="color: #000080;">-d</span> dbg.raw.fa <span class="nt" style="color: #000080;">-i</span> - <span class="nt" style="color: #000080;">-fo</span> dbg.cns.fa</span>
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<td class="diff-line-num old old_line" data-linenumber="33" 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="LC33" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> dbg.cns.fa <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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<td class="diff-line-num old old_line" data-linenumber="34" 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="LC34" 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="LC35" class="line" lang="shell"></span></pre>
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