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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/covtobed">Debian Med / covtobed</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/7d8b9a86bb8edc8e0b091be9d7e8db81e97a37f5">7d8b9a86</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-26T02:14:09+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/e378a0cd66fceb3de0332c307fabf12d22d2ab6e">e378a0cd</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-26T02:14:17+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/7a9b2740716477ba2a9793d640598301679a7389">7a9b2740</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-26T02:14:49+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.0+dfsg'
Update to upstream version '1.2.0+dfsg'
with Debian dir 3c718954f69fbb1181118fc9fcf91d48a980542a</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/7ea23558f5e2401205a07508623dd337b903b721">7ea23558</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-26T02:16:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/eb142ae7778fae4af2b16cd2e29a00a579a1b215">eb142ae7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-26T02:20:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#d4f363b12339afef2d776bb54337618051dc0857">
base.cpp
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/ad6b0ebabd47531de0c82c5d2719bafaa631823f...eb142ae7778fae4af2b16cd2e29a00a579a1b215#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># covtobed</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![License</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://img.shields.io/github/license/telatin/covtobed?color=blue</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://github.com/telatin/covtobed/blob/master/LICENSE)</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/<span class="idiff left right">badge/install%20with-bioconda-brightgreen.svg?style=flat</span></span><span class="p">)</span>](http://bioconda.github.io/recipes/covtobed/README.html)</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"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/<span class="idiff left right">conda/vn/bioconda/covtobed?label=install%20from%20bioconda</span></span><span class="p">)</span>](http://bioconda.github.io/recipes/covtobed/README.html)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Bioconda installs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/covtobed</span><span class="p">)</span>](https://anaconda.org/bioconda/covtobed)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![TravisCI Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/telatin/covtobed.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/telatin/covtobed)</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker build</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/<span class="idiff left right">cloud/build</span>/andreatelatin/covtobed</span><span class="p">)</span>](https://hub.docker.com/r/andreatelatin/covtobed)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Codacy Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://app.codacy.com/project/badge/Grade/36944efb0d2b44cca850964e96c036a4</span><span class="p">)</span>](https://www.codacy.com/manual/telatin/covtobed?utm_source=github.com<span class="ni" style="color: #800080;">&</span>utm_medium=referral<span class="ni" style="color: #800080;">&</span>utm_content=telatin/covtobed<span class="ni" style="color: #800080;">&</span>utm_campaign=Badge_Grade)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### a tool to generate BED coverage tracks from BAM files</span></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">@@ -15,6 +17,10 @@ Reads one (or more) [alignment](https://en.wikipedia.org/wiki/Sequence_alignment</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown">:book: <span class="gs" style="font-weight: 600;">**[Read more in the wiki](https://github.com/telatin/covtobed/wiki)**</span> - this is the <span class="gs" style="font-weight: 600;">**main**</span> documentation source</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">Features:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">*</span> Can read (sorted) BAMs from stream (like <span class="sb" style="color: #d14;">`bwa mem .. | samtools view -b | samtools sort - | covtobed`</span>)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">*</span> Can print _strand specific_ coverage to check for strand imbalance</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">*</span> Can print the _physical coverage_ (with paired-end or mate-paired libraries)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![covtobed example</span><span class="p">](</span><span class="sx" style="color: #d14;">img/covtobed-vignette.png</span><span class="p">)</span>](https://github.com/telatin/covtobed/wiki)</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></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">@@ -45,6 +51,8 @@ Options:</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"> -l MINLEN, --min-len=MINLEN</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"> print BED feature only if its length is bigger (or equal</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"> to) than MINLELN (default: 1)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"> -z MINCTG, --min-ctg-len=MINCTG</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"> skip reference sequences having size less or equal to MINCTG</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"> -d, --discard-invalid-alignments</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"> skip duplicates, failed QC, and non primary alignment,</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"> minq>0 (or user-defined if higher) (default: 0)</span>
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<li id="d4f363b12339afef2d776bb54337618051dc0857">
<a href="https://salsa.debian.org/med-team/covtobed/-/compare/ad6b0ebabd47531de0c82c5d2719bafaa631823f...eb142ae7778fae4af2b16cd2e29a00a579a1b215#d4f363b12339afef2d776bb54337618051dc0857"><strong>base.cpp</strong></a>
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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">@@ -16,7 +16,7 @@ using namespace std;</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">DepthType</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// type for depth of coverage, kept it small</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ref_char</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// reference prefix for "counts" output</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%prog 1.<span class="idiff left right">1.4</span>"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%prog 1.<span class="idiff left right">2.0</span>"</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Copyright (C) 2014-2019 Giovanni Birolo and Andrea Telatin</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="s" style="color: #d14;">"https://github.com/telatin/covtobed - License MIT"</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="s" style="color: #d14;">".</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" 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="192" 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">@@ -192,6 +192,7 @@ int main(int argc, char *argv[]) {</td>
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192
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<td class="diff-line-num new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--min-cov"</span><span class="p">).</span><span class="n" style="color: #333;">metavar</span><span class="p">(</span><span class="s" style="color: #d14;">"MINCOV"</span><span class="p">).</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="s" style="color: #d14;">"int"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"0"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"print BED feature only if the coverage is bigger than (or equal to) MINCOV (default: %default)"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="193" 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">
193
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<td class="diff-line-num new_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-x"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--max-cov"</span><span class="p">).</span><span class="n" style="color: #333;">metavar</span><span class="p">(</span><span class="s" style="color: #d14;">"MAXCOV"</span><span class="p">).</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="s" style="color: #d14;">"int"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"100000"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"print BED feature only if the coverage is lower than MAXCOV (default: %default)"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="194" 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">
194
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<td class="diff-line-num new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-l"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--min-len"</span><span class="p">).</span><span class="n" style="color: #333;">metavar</span><span class="p">(</span><span class="s" style="color: #d14;">"MINLEN"</span><span class="p">).</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="s" style="color: #d14;">"int"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"print BED feature only if its length is bigger (or equal to) than MINLELN (default: %default)"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="195" 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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<td class="diff-line-num new new_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-z"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--min-ctg-len"</span><span class="p">).</span><span class="n" style="color: #333;">metavar</span><span class="p">(</span><span class="s" style="color: #d14;">"MINCTGLEN"</span><span class="p">).</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="s" style="color: #d14;">"int"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"Skip reference sequences (contigs) shorter than this value"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="195" 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">
195
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<td class="diff-line-num new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--discard-invalid-alignments"</span><span class="p">).</span><span class="n" style="color: #333;">action</span><span class="p">(</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">).</span><span class="n" style="color: #333;">set_default</span><span class="p">(</span><span class="s" style="color: #d14;">"0"</span><span class="p">).</span><span class="n" style="color: #333;">help</span><span class="p">(</span><span class="s" style="color: #d14;">"skip duplicates, failed QC, and non primary alignment, minq>0 (or user-defined if higher) (default: %default)"</span><span class="p">);</span></span>
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196
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"></span>
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197
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="208" 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="209" 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">@@ -208,6 +209,7 @@ int main(int argc, char *argv[]) {</td>
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208
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<td class="diff-line-num new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimum_coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_cov"</span><span class="p">);</span></span>
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209
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<td class="diff-line-num new_line" data-linenumber="210" 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">
210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maximum_coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"max_cov"</span><span class="p">);</span></span>
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210
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<td class="diff-line-num new_line" data-linenumber="211" 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">
211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_len"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="212" 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">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimum_contig_len</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_ctg_len"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="211" 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">
211
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<td class="diff-line-num new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"min_mapq"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">only_valid</span> <span class="n" style="color: #333;">and</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">min_mapq</span><span class="p">)</span> <span class="p">{</span></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">@@ -232,6 +234,9 @@ int main(int argc, char *argv[]) {</td>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">get_ref_data</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// loop on reference</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// init new reference data</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">get_ref_id</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefName</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefLength</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">minimum_contig_len</span><span class="p">)</span> <span class="p">{</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">debug</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[R] Reference: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ref_id</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">PositionType</span> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">priority_queue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CovEnd</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">coverage_ends</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">covtobed (1.2.0+dfsg-1) 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"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Mon, 26 Oct 2020 02:15:17 +0530</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">covtobed (1.1.4+dfsg-2) unstable; urgency=medium</span>
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2
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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"> * Fix FTCBFS: Let dpkg's buildtools.mk setup cross tools (Closes: #970829)</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: covtobed</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Shayan Doust <hello@shayandoust.me></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Shayan Doust <hello@shayandoust.me><span class="idiff left right">, Nilesh Patra <npatra974@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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