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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/tiddit">Debian Med / tiddit</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/tiddit/-/commit/c4a6394cc9783aaf8f8dbbd39055cee2d5256946">c4a6394c</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-06-28T14:07:17+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix tests
</pre>
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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/tiddit/-/commit/c4a6394cc9783aaf8f8dbbd39055cee2d5256946#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="17" 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="17" 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">@@ -17,12 +17,10 @@ cat normal.sam | samtools view -Sb - > normal.bam</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>tumor.sam | samtools view <span class="nt" style="color: #000080;">-Sb</span> - <span class="o" style="font-weight: 600;">></span> tumor.bam</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC18" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 1'</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">TIDDIT.py <span class="nt" style="color: #000080;">--sv</span> <span class="nt" style="color: #000080;">--p_ratio</span> 0.10 <span class="nt" style="color: #000080;">--bam</span> tumor.bam <span class="nt" style="color: #000080;">-o</span> tumor <span class="nt" style="color: #000080;">--ref</span> ref.fa</span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>tumor.pass.vcf</span>
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<td class="diff-line-num new old_line" data-linenumber="22" 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="LC20" class="line" lang="shell">TIDDIT.py <span class="nt" style="color: #000080;">--sv</span> <span class="nt" style="color: #000080;">--p_ratio</span> 0.10 <span class="nt" style="color: #000080;">--bam</span> tumor.bam <span class="nt" style="color: #000080;">-o</span> test1 <span class="nt" style="color: #000080;">--ref</span> ref.fa</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="s1" style="color: #d14;">'PASS'</span></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 class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 2'</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">TIDDIT.py <span class="nt" style="color: #000080;">--sv</span> <span class="nt" style="color: #000080;">--bam</span> normal.bam <span class="nt" style="color: #000080;">-o</span> normal <span class="nt" style="color: #000080;">--ref</span> ref.fa</span>
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<td class="diff-line-num old old_line" data-linenumber="26" 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="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>normal.pass.vcf</span>
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<td class="diff-line-num new old_line" data-linenumber="27" 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="LC24" class="line" lang="shell">TIDDIT.py <span class="nt" style="color: #000080;">--sv</span> <span class="nt" style="color: #000080;">--bam</span> normal.bam <span class="nt" style="color: #000080;">-o</span> test2 <span class="nt" style="color: #000080;">--ref</span> ref.fa</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span></pre>
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