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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:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/6a3f44079c7fbf940d5340ec4874b08f89f91ff4">6a3f4407</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-08-09T20:51:54+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Simplify autopkgtest
</pre>
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<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/7f3984e67ca50a450205c92719a6d5de3bc704b1">7f3984e6</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-08-09T20:55:22+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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<li class="file-stats">
<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/wtdbg2/-/compare/e56ba7735427e54e99ee73d083a4ee8a78724aa2...7f3984e67ca50a450205c92719a6d5de3bc704b1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">wtdbg2 (2.5-4) UNRELEASED; 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"> * Save up space by not extracting the binary</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * New binary: wtdbg2-examples</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Minor fixes on manpages</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fix spellings</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"> -- Nilesh Patra <npatra974@gmail.com> Sun, 09 Aug 2020 20:28:18 +0530</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">wtdbg2 (2.5-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/e56ba7735427e54e99ee73d083a4ee8a78724aa2...7f3984e67ca50a450205c92719a6d5de3bc704b1#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="15" 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="15" 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">@@ -15,14 +15,6 @@ gunzip -r *</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">-xvf</span> <span class="k" style="font-weight: 600;">*</span>.tar</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>selfSampleData</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Checks whether file checksum is same as expected</span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>check_same<span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># $1 : file name</span></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;"># $2 : checksum value</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$1</span> | <span class="nb" style="color: #0086b3;">md5sum</span> | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{print $1}'</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: #008080;">$2</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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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"></span>
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26
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Begin Execution"</span></span>
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27
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell">wtdbg2 <span class="nt" style="color: #000080;">-t</span> 16 <span class="nt" style="color: #000080;">-x</span> rs <span class="nt" style="color: #000080;">-g</span> 4.6m <span class="nt" style="color: #000080;">-o</span> dbg pacbio_filtered.fastq</span>
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28
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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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">@@ -32,12 +24,12 @@ wtdbg2 -x rs -g 4.6m -i pacbio_filtered.fastq -t 16 -fo dbg</td>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># derive consensus</span></span>
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34
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell">wtpoa-cns <span class="nt" style="color: #000080;">-t</span> 16 <span class="nt" style="color: #000080;">-i</span> dbg.ctg.lay.gz <span class="nt" style="color: #000080;">-fo</span> dbg.raw.fa</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="idiff left right">check_same dbg.raw.fa a2c479242d7c6ad6c8ffd979b821aa0</span>1</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="o" style="font-weight: 600;"><span class="idiff left">[</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> dbg.raw.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">exit </span></span>1</span>
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36
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28
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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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37
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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38
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30
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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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39
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31
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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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40
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32
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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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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"><span class="idiff left right">check_same dbg.cns.fa 62a41e5cb7a5e702523237f4ab65c376</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="o" style="font-weight: 600;"><span class="idiff left">[</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff"> dbg.cns.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">exit </span></span><span class="idiff right">1</span></span>
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42
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34
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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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43
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"></span></pre>
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