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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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<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/eafa7abbf1d586c4b77f82bb4ba72cc0aab00ecf">eafa7abb</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-06T22:41:10+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Simplify autopkgtest (Closes: #964101)
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<strong><a href="https://salsa.debian.org/med-team/tiddit/-/commit/a14b79445d0e403f5eddbfc9f1983c177996929b">a14b7944</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-06T22:44:59+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>4 changed files:</h4>
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debian/changelog
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<a href="#34a4bd40604738654f7f15305b508c03c040114d">
debian/tests/README.md
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debian/tests/data/ref.fa
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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/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tiddit (2.12.0+dfsg-3) UNRELEASED; urgency=medium</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"> * Simplify autopkgtest (Closes: #964101)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Tue, 06 Oct 2020 22:41:27 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">tiddit (2.12.0+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team Upload.</span>
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<li id="34a4bd40604738654f7f15305b508c03c040114d">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b#34a4bd40604738654f7f15305b508c03c040114d"><strong>debian/tests/README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Data for tiddit</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=====================</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">The data is from NA12878 (tumor) and NA12892 (normal) and represents a tiny chunk of chromsome 21. It was created from 1000 Genomes Project (http://www.1000genomes.org) data available in the following locations:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="p">*</span> NA12892 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12892/high_coverage_alignment/NA12892.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">*</span> NA12878 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">*</span> Build 37 reference - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"> The test data for tiddit has been referenced from here: https://github.com/genome/somatic-snv-test-data which has further steps for creating the data</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"> All work is from public datasets and have been made with tools in the open domain.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span></pre>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">Should you wish to recreate the files in this repository, they were processed as follows below.</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;"> samtools view -hb NA12892.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam 21:10400000-10500000 > normal.bam</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="sb" style="color: #d14;"> samtools view -hb NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam 21:10400000-10500000 > tumor.bam</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="sb" style="color: #d14;"> gunzip human_g1k_v37.fasta.gz</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="sb" style="color: #d14;"> samtools faidx human_g1k_v37.fasta 21:1-10505000 > ref.fa</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="sb" style="color: #d14;"> samtools view -h -o normal.sam normal.bam</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;"> samtools view -h -o tumor.sam tumor.bam</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">Note that ref.fa was then further edited to change the chromosome name back to 21 as faidx includes the requested region in the name.</span></pre>
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<li id="0621768541f66261c3ccdebade9959d428fa36cd">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b#0621768541f66261c3ccdebade9959d428fa36cd"><strong>debian/tests/data/ref.fa</strong>
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The diff for this file was not included because it is too large.
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<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">@@ -17,10 +17,24 @@ 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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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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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20
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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="LC20" class="line" lang="shell">TIDDIT <span class="nt" style="color: #000080;">--cov</span> <span class="nt" style="color: #000080;">-b</span> normal.bam <span class="nt" style="color: #000080;">-o</span> test1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">TIDDIT <span class="nt" style="color: #000080;">--cov</span> <span class="nt" style="color: #000080;">-w</span> <span class="nt" style="color: #000080;">-b</span> normal.bam <span class="nt" style="color: #000080;">-o</span> test1</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>f <span class="k" style="font-weight: 600;">in </span>test1.<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$f</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$f</span> | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-20</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./test1<span class="k" style="font-weight: 600;">*</span></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="s1" style="color: #d14;">'PASS'</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></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="s1" style="color: #d14;">'Test 2'</span></span>
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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="LC31" class="line" lang="shell">TIDDIT <span class="nt" style="color: #000080;">--cov</span> <span class="nt" style="color: #000080;">-b</span> normal.bam <span class="nt" style="color: #000080;">-o</span> test2</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">TIDDIT <span class="nt" style="color: #000080;">--cov</span> <span class="nt" style="color: #000080;">-w</span> <span class="nt" style="color: #000080;">-b</span> tumor.bam <span class="nt" style="color: #000080;">-o</span> test2</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>f <span class="k" style="font-weight: 600;">in </span>test2.<span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$f</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$f</span> | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-20</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./test2<span class="k" style="font-weight: 600;">*</span></span>
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25
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<pre style="margin: 0;"> <span id="LC39" 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="LC40" class="line" lang="shell"></span></pre>
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