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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/covtobed">Debian Med / covtobed</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/covtobed/-/commit/67aa1fbca9e3e37bd888f184c377867a3ad5a13f">67aa1fbc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-09-22T18:25:28+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.4+dfsg</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#3f454a98e586d1aa0d322e19afd5e67e08f2d3c8">
CONTRIBUTING.md
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<li class="file-stats">
<a href="#d4f363b12339afef2d776bb54337618051dc0857">
base.cpp
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<li class="file-stats">
<a href="#3783a7caccbf26cc060ec5fce01fb0a22bded3dd">
benchmark/disk_file.sh
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/67aa1fbca9e3e37bd888f184c377867a3ad5a13f#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,3 +18,6 @@ pannelli</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">paper/paper.md~</span>
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<td class="diff-line-num new_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="plaintext">TE</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">split_sam_by_flag.pl</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">mini_tests</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.vscode</span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">prova.sh</span></pre>
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<li id="3f454a98e586d1aa0d322e19afd5e67e08f2d3c8">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/67aa1fbca9e3e37bd888f184c377867a3ad5a13f#3f454a98e586d1aa0d322e19afd5e67e08f2d3c8"><strong>CONTRIBUTING.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown">If you wish to fix a bug or add new features to the software we welcome Pull Requests. </span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Contributing to `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">If you wish to fix a bug or add new features to the software we welcome <span class="gs" style="font-weight: 600;">**Pull Requests**</span>. </span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">We use <span class="p">[</span><span class="nv" style="color: #008080;">GitHub Flow style development</span><span class="p">](</span><span class="sx" style="color: #d14;">https://guides.github.com/introduction/flow/</span><span class="p">)</span>. </span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<li id="d4f363b12339afef2d776bb54337618051dc0857">
<a href="https://salsa.debian.org/med-team/covtobed/-/commit/67aa1fbca9e3e37bd888f184c377867a3ad5a13f#d4f363b12339afef2d776bb54337618051dc0857"><strong>base.cpp</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="idiff left right"> </span><span class="cp" style="color: #999; font-weight: 600;">#include <queue></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <queue></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <map></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="16" 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">@@ -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 1.1.<span class="idiff left right">2</span>"</span></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 1.1.<span class="idiff left right">4</span>"</span></span>
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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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<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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<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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,11 +61,17 @@ class Input {</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">get_next_alignment</span><span class="p">(</span><span class="n" style="color: #333;">BamAlignment</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">more_alignments</span><span class="p">,</span> <span class="n" style="color: #333;">good_alignment</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">"[M] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">Name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">Position</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" | Is mapped? "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsMapped</span><span class="p">()</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="LC64" 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;">"[M] Read on ref#"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">RefID</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" pos:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">Position</span> <span class="o" style="font-weight: 600;"><<</span> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">| Is mapped? "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsMapped</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" | AlignmentFlag:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">AlignmentFlag</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="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">more_alignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_bams</span><span class="p">.</span><span class="n" style="color: #333;">GetNextAlignmentCore</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">discard_invalid_alignments</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">good_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsMapped</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">MapQuality</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_mapq</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsDuplicate</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsFailedQC</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsPrimaryAlignment</span><span class="p">()</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsDuplicate</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsFailedQC</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsPrimaryAlignment</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1.2.0 ProperPair</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsPaired</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsProperPair</span><span class="p">()</span> <span class="p">)</span> <span class="p">{</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">good_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="p">}</span></span>
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69
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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70
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">good_alignment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsMapped</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">MapQuality</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">;</span></span>
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71
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="216" 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">@@ -210,6 +216,7 @@ int main(int argc, char *argv[]) {</td>
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210
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <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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211
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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214
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// open input and output</span></span>
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215
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">Input</span> <span class="n" style="color: #333;">input</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">(),</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span> <span class="n" style="color: #333;">only_valid</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" 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="254" 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">@@ -247,6 +254,7 @@ int main(int argc, char *argv[]) {</td>
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247
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">more_alignments_for_ref</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">next_change</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">Position</span><span class="p">)</span> <span class="p">{</span></span>
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248
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">physical_coverage</span><span class="p">)</span> <span class="p">{</span></span>
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249
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">InsertSize</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" 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;">" [phy] pos:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">Position</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" size:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">InsertSize</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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250
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<td class="diff-line-num new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">coverage_ends</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">({</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">Position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">InsertSize</span><span class="p">,</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsReverseStrand</span><span class="p">()});</span></span>
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251
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">inc</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">IsReverseStrand</span><span class="p">());</span></span>
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252
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="274" 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">@@ -266,9 +274,13 @@ int main(int argc, char *argv[]) {</td>
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266
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274
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<pre style="margin: 0;"> <span id="LC274" 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;">"[<] Coverage is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" from "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">next_change</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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267
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_change</span><span class="p">;</span></span>
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268
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<td class="diff-line-num new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefLength</span><span class="p">);</span></span>
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269
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<td class="diff-line-num new_line old" data-linenumber="277" 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="LC269" 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;">"[_] Completed at "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">last_pos</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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<td class="diff-line-num new old_line" data-linenumber="270" 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="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" 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;">"[_] Completed at "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;"><span class="idiff left">" [coverage:"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">coverage_ends</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><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="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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270
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<td class="diff-line-num new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reference ended</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">coverage_ends</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">());</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">coverage_ends</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Coverage is not zero at the end of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">RefName</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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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Try samtools fixmate on the input file"</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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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="p">}</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 1.2.0 -- removed: assert(coverage_ends.empty());</span></span>
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272
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="p">}</span></span>
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273
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//assert(!more_alignments);</span></span>
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274
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">more_alignments</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/covtobed/-/commit/67aa1fbca9e3e37bd888f184c377867a3ad5a13f#3783a7caccbf26cc060ec5fce01fb0a22bded3dd"><strong>benchmark/disk_file.sh</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">@@ -20,14 +20,13 @@ if [ ! -e "$FILE" ]; then</td>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left right"> </span></span><span class="nv" style="color: #008080;">TAG</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$FILE</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1</span> <span class="nt" style="color: #000080;">-d</span>.<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">TAG</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$FILE</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1</span> <span class="nt" style="color: #000080;">-d</span>.<span class="si" style="color: #d14;">)</span></span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="idiff left right"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TAG</span><span class="s2" style="color: #d14;"> [</span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;">]"</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="idiff left right"> </span>hyperfine <span class="nt" style="color: #000080;">--warmup</span> 2 <span class="nt" style="color: #000080;">--min-runs</span> 6 <span class="nt" style="color: #000080;">--cleanup</span> <span class="s1" style="color: #d14;">'rm *.bed mos?_*.* || true'</span> <span class="se" style="color: #d14;">\</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TAG</span><span class="s2" style="color: #d14;"> [</span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;">]"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">hyperfine <span class="nt" style="color: #000080;">--warmup</span> 2 <span class="nt" style="color: #000080;">--min-runs</span> 6 <span class="nt" style="color: #000080;">--cleanup</span> <span class="s1" style="color: #d14;">'rm *.bed mos?_*.* || true'</span> <span class="se" style="color: #d14;">\</span></span>
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27
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"> <span class="nt" style="color: #000080;">--export-markdown</span> disk_<span class="nv" style="color: #008080;">$TAG</span>.md <span class="se" style="color: #d14;">\</span></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"> <span class="s2" style="color: #d14;">"mosdepth -F 4 -x -t 4 mos4_ </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"> <span class="s2" style="color: #d14;">"mosdepth -F 4 -x mos1_ </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"> <span class="s2" style="color: #d14;">"covtobed </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;"> > covtobed_</span><span class="nv" style="color: #008080;">$TAG</span><span class="s2" style="color: #d14;">.bed"</span> <span class="se" style="color: #d14;">\</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"> <span class="s2" style="color: #d14;">"sambamba depth base -F 'not unmapped' </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;"> > sambamba.txt.bed"</span> <span class="se" style="color: #d14;">\</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"> <span class="s2" style="color: #d14;">"sambamba depth window -F 'not unmapped' -w 1000 </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;"> > sambamba2.txt.bed"</span><span class="se" style="color: #d14;">\</span></span>
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33
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"> <span class="s2" style="color: #d14;">"bedtools genomecov -bga -ibam </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;"> > bedtools_</span><span class="nv" style="color: #008080;">$TAG</span><span class="s2" style="color: #d14;">.bed"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span></pre>
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