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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mosdepth">Debian Med / mosdepth</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de">4466b303</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-11-02T22:39:00+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.1</pre>
</li>
</ul>
<h4>13 changed files:</h4>
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<li class="file-stats">
<a href="#fe77d5d1439f26e353a42bbd38dece2467ff6558">
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+
.github/workflows/build.yml
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#98f5d7ecd16412a1f8781d3d8c896dd0323a69af">
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+
depthstat.nim
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<li class="file-stats">
<a href="#5e05ccb32e2de6797c54768d95e4cc3ba8c8bc5f">
functional-tests.sh
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<li class="file-stats">
<a href="#3a6852ca596d0b268c25ad8cb502054fb3405cac">
<span class="new-file">
+
int2str.nim
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<li class="file-stats">
<a href="#f2a4f454974b64d881d2a470683d1c37fb1aa2bb">
mosdepth.nim
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<li class="file-stats">
<a href="#a99b7e9ffb6c06b4832f1c7ce8d8dbbf023f7502">
mosdepth.nimble
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<li class="file-stats">
<a href="#1f022802374dbfb04433943a561ed4b5f0e0aa25">
scripts/install.sh
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<li class="file-stats">
<a href="#ec55c77e5315f22521ed1a772a398adb082f28e3">
scripts/plot-dist.py
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<li class="file-stats">
<a href="#5c05cfa4f939f387afdf0c5360196139984517fd">
tests/funcs.nim
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<h4>Changes:</h4>
<li id="fe77d5d1439f26e353a42bbd38dece2467ff6558">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#fe77d5d1439f26e353a42bbd38dece2467ff6558"><strong>.github/workflows/build.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># copied from Daniel Cook's Seq collection</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">push</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pull_request</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-18.04</span><span class="pi">,</span> <span class="nv" style="color: #008080;">macos-10.15</span><span class="pi">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">nimversion</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">stable</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">devel</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Caching</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Cache choosenim</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #d14;">cache-choosenim</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/cache@v1</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">~/.choosenim</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">key</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ runner.os }}-choosenim-stable</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Cache nimble</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #d14;">cache-nimble</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/cache@v1</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">~/.nimble</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">key</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ runner.os }}-nimble-stable</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Cache htslib</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #d14;">cache-htslib</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/cache@v1</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">$HOME/htslib</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">key</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ runner.os }}-htslib-1.10</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Install Dependencies</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install dependencies (Linux)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">runner.os == 'Linux'</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get update</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="s" style="color: #d14;">curl libssl-dev libtool autoconf automake libcurl4-openssl-dev</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install d4</span> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="s" style="color: #d14;">git clone https://github.com/38/d4-format</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd d4-format</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="s" style="color: #d14;">cargo build --release</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo cp ../d4-format/target/release/libd4binding.* /usr/local/lib</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo cp ./d4binding/include/d4.h /usr/local/include/</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Setup htslib</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install htslib (linux)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">runner.os == 'Linux'</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="s" style="color: #d14;">git clone --recursive https://github.com/samtools/htslib.git</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="s" style="color: #d14;">make -j 4 -C htslib</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="s" style="color: #d14;">echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="s" style="color: #d14;">ls -lh $HOME/htslib/*.so</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="yaml"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install hstlib (macos)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">runner.os == 'macOS'</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="yaml"> <span class="s" style="color: #d14;">brew install htslib</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="yaml"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">iffy/install-nim@v1.1</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml"> <span class="na" style="color: #008080;">nimversion</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.nimversion }}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="yaml"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions-rs/toolchain@v1</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="yaml"> <span class="na" style="color: #008080;">toolchain</span><span class="pi">:</span> <span class="s" style="color: #d14;">stable</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions-rs/cargo@v1</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="yaml"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Build and Test</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build test executable</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">nimble build -Y mosdepth.nimble</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="yaml"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Copy</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">binary"</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="yaml"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">and</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Copy</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">release</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">binary"</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">nim c -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="yaml"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Functional Tests</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="yaml"> <span class="na" style="color: #008080;">TERM</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">xterm"</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="yaml"> <span class="s" style="color: #d14;">bash ./functional-tests.sh</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="yaml"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Unit Tests</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="yaml"> <span class="s" style="color: #d14;">nim c -r tests/all.nim</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="yaml"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Upload Artifact</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">success()</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/upload-artifact@v1.0.0</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">mosdepth_${{ matrix.os }}_executable</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">bin/</span></span></pre>
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<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">nimcache</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">*.d4</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">*.bam</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">*.cram</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">*.bai</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">@@ -6,3 +7,6 @@ nimcache</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">profile_results.txt</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">t.*.bed.gz</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">t.*.bed.gz.csi</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">*.bed.gz*</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">*.dist.txt</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">*.summary.txt</span></pre>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -3,7 +3,7 @@ env:</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">BRANCH=devel</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export LD_LIBRARY_PATH=./htslib<span class="idiff left right">/</span></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export LD_LIBRARY_PATH=./htslib<span class="idiff left right">-1.10.2/:/usr/local/lib</span></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$TRAVIS_BUILD_DIR/nim-$BRANCH/bin:$PATH"</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export NIM_LIB_PREFIX=$TRAVIS_BUILD_DIR/nim-$BRANCH/</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" 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>
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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">@@ -12,6 +12,7 @@ install:</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nimble test</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash functional-tests.sh</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nim c -r depthstat.nim</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">nim c -d:release --cc:$CC mosdepth.nim</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./mosdepth -h</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"><span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">0.2.5 (dev)</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.1</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">+</span> fix bug with regions and d4 that would cause error even when --d4 was not used.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.0</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">+</span> allow chromosome names containing '-' as arguments for -c</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">+</span> d4 output</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">0.</span>2.9</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">=====</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">+</span> modifies region.dist.txt to contain the aggregate coverage of each window when -b (integer) is specified</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"> (otherwise region.dist.txt and global.disk.txt are identical with -b (integer) )</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">+</span> improve speed by ~30% when using per-base output with better int2str method</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> </span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">0.</span>2.8</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">=====</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">+</span> fix off-by-one error in CSI index (but not data) of output bed files (#98)</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">0.</span>2.7</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">=====</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">+</span> small optimizations</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">+</span> exit with 1 on bad help #80</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p">+</span> fix check on remote bam (brentp/hts-nim#48)</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">+</span> fix erroneous assert #99</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">+</span> update static binary to htslib 1.10 (this fixes other bugs reported and closed in mosdepth)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p">0.</span>2.6</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">=====</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">+</span> fix #54. for quantize</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">+</span> add summary file output (implemented by @danielecook)</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">+</span> add <span class="sb" style="color: #d14;">`--median`</span> flag to output the median for each region from --by (default is to use mean).</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">0.</span>2.5</span>
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2
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown">=====</span>
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3
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">+</span> remove dependency on PCRE</span>
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4
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="p">+</span> don't double count fully overlapping reads (thanks to @jaudoux for the fix in #73)</span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -4,7 +4,8 @@ fast BAM/CRAM depth calculation for **WGS**, **exome**, or **targeted sequencing</td>
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4
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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"><span class="p">![</span><span class="nv" style="color: #008080;">logo</span><span class="p">](</span><span class="sx" style="color: #d14;">https://user-images.githubusercontent.com/1739/29678184-da1f384c-88ba-11e7-9d98-df4fe3a59924.png</span> <span class="nn" style="color: #555;">"logo"</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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/brentp/mosdepth.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/brentp/mosdepth)</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;">![Build</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/mosdepth/workflows/Build/badge.svg?branch=master</span><span class="p">)</span>](https://github.com/brentp/mosdepth/actions?query=workflow%3ABuild)</span>
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8
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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;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.com/brentp/mosdepth.svg?branch=master</span><span class="p">)</span>](https://travis-ci.com/brentp/mosdepth)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![citation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/cite-open%20access-orange.svg</span><span class="p">)</span>](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx699/4583630?guestAccessKey=35b55064-4566-4ab3-a769-32916fa1c6e6)</span>
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<pre style="margin: 0;"> <span id="LC11" 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">@@ -13,24 +14,28 @@ fast BAM/CRAM depth calculation for **WGS**, **exome**, or **targeted sequencing</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p">+</span> per-base depth about 2x as fast <span class="sb" style="color: #d14;">`samtools depth`</span>--about 25 minutes of CPU time for a 30X genome.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p">+</span> mean per-window depth given a window size--as would be used for CNV calling.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">+</span> the mean per-region given a BED file of regions.</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="p">+</span> a distribution of proportion of bases covered at or above a given threshhold for each chromosome and genome-wide.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">*</span> the mean or median per-region cumulative coverage histogram given a window size</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">+</span> a distribution of proportion of bases covered at or above a given threshold for each chromosome and genome-wide.</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">+</span> quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p">+</span> threshold output to indicate how many bases in each region are covered at the given thresholds.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">+</span> A summary of mean depths per chromosome and within specified regions per chromosome.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">+</span> a <span class="p">[</span><span class="nv" style="color: #008080;">d4</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/38/d4-format</span><span class="p">)</span> file (better than bigwig).</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown">when appropriate, the output files are bgzipped and indexed for ease of use.</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## usage</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">mosdepth 0.<span class="idiff left right">2.3</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">mosdepth 0.<span class="idiff left right">3.0</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"> Usage: mosdepth [options] <prefix> <BAM-or-CRAM></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown">Arguments:</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"> <prefix> outputs: `{prefix}.mosdepth.global.dist.txt` (NOTE!!! this is changed in version 0.2.2)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"> <prefix> outputs: `{prefix}.mosdepth.global.dist.txt`</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"> `{prefix}.mosdepth.summary.txt`</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"> `{prefix}.mosdepth.region.dist.txt` (if --by is specified)</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"> `{prefix}.per-base.bed.gz` (unless -n/--no-per-base is specified)</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"> `{prefix}.per-base.bed.gz<span class="idiff left right">|per-base.d4</span>` (unless -n/--no-per-base is specified)</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"> `{prefix}.regions.bed.gz` (if --by is specified)</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"> `{prefix}.quantized.bed.gz` (if --quantize is specified)</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"> `{prefix}.thresholds.bed.gz` (if --thresholds is specified)</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 +50,8 @@ Common Options:</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"> -n --no-per-base dont output per-base depth. skipping this output will speed execution</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"> substantially. prefer quantized or thresholded values if possible.</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"> -f --fasta <fasta> fasta file for use with CRAM files.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"> --d4 output per-base depth in d4 format. This is much faster.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown">Other options:</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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="59" 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">@@ -52,7 +59,7 @@ Other options:</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"> -i --include-flag <FLAG> only include reads with any of the bits in FLAG set. default is unset. [default: 0]</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"> -x --fast-mode dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"> -q --quantize <segments> write quantized output see docs for description.</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"> -Q --mapq <mapq> mapping quality threshold [default: 0]</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"> -Q --mapq <mapq> mapping quality threshold<span class="idiff left right">. reads with a mapping quality less than this are ignored</span> [default: 0]</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"> -T --thresholds <thresholds> for each interval in --by, write number of bases covered by at</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"> least threshold bases. Specify multiple integer values separated</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"> by ','.</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">@@ -131,9 +138,21 @@ Output will go to `$sample.mosdepth.dist.txt`</td>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown">This also forces the output to have 5 decimals of precision rather than the default of 2.</span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## D4</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown">D4 is a format created by <span class="p">[</span><span class="nv" style="color: #008080;">Hao Hou</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/38</span><span class="p">)</span> in the Quinlan lab. It is</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown">incorporated into <span class="sb" style="color: #d14;">`mosdepth`</span> as of version 0.3.0 for per-base output with the <span class="sb" style="color: #d14;">`--d4`</span> flag.</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown">It improves write speed dramatically; for one test-case it takes <span class="gs" style="font-weight: 600;">**24.8s**</span> to write a</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown">per-base.bed.gz with mosdepth compared to <span class="gs" style="font-weight: 600;">**7.7s**</span> to write a d4 file. For the same case,</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown">running <span class="sb" style="color: #d14;">`mosdepth`</span> without writing per-base takes 5.9 seconds so D4 greatly mitigates</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown">the cost of outputing per-base depth <span class="gs" style="font-weight: 600;">**and**</span> the output is more useful.</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="markdown">The simplest way is to <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/badge/install%20with-bioconda-brightgreen.svg?style=flat-square</span><span class="p">)</span>](http://bioconda.github.io/recipes/mosdepth/README.html)</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown">The simplest option is to download the <span class="p">[</span><span class="nv" style="color: #008080;">binary from the releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/mosdepth/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown">Another quick way is to <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/badge/install%20with-bioconda-brightgreen.svg?style=flat-square</span><span class="p">)</span>](http://bioconda.github.io/recipes/mosdepth/README.html)</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown">It can also be installed with <span class="sb" style="color: #d14;">`brew`</span> as <span class="sb" style="color: #d14;">`brew install brewsci/bio/mosdepth`</span> or used via docker with quay:</span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown"><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">@@ -141,10 +160,8 @@ docker pull quay.io/biocontainers/mosdepth:0.2.4--he527e40_0</td>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="markdown">docker run -v /hostpath/:/opt/mount quay.io/biocontainers/mosdepth:0.2.4--he527e40_0 mosdepth -n --fast-mode -t 4 --by 1000 /opt/mount/sample /opt/mount/$bam</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="markdown">Unless you want to install <span class="p">[</span><span class="nv" style="color: #008080;">nim</span><span class="p">](</span><span class="sx" style="color: #d14;">https://nim-lang.org</span><span class="p">)</span>, simply download the</span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">binary from the releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/mosdepth/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mosdepth`</span> uses requires htslib version 1.4 or later. If you get an error</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown">The binary from releases is static, with no dependencies. If you build it yourself,</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mosdepth`</span> requires htslib version 1.4 or later. If you get an error</span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="markdown">about "<span class="sb" style="color: #d14;">`libhts.so`</span> not found", set <span class="sb" style="color: #d14;">`LD_LIBRARY_PATH`</span> to the directory that</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="markdown">contains <span class="sb" style="color: #d14;">`libhts.so`</span>. e.g.</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" 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="170" 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">@@ -153,25 +170,6 @@ contains `libhts.so`. e.g.</td>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown">If you get the error <span class="sb" style="color: #d14;">`could not import: hts_check_EOF`</span> you may need to</span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown">install a more recent version of htslib.</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mosdepth`</span> also requires a recent version of <span class="p">[</span><span class="nv" style="color: #008080;">PCRE</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.pcre.org/</span><span class="p">)</span>, and will give the error <span class="sb" style="color: #d14;">`could not import: pcre_free_study`</span> if the version of PCRE on your system is too old.</span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="markdown">If you do not have root and cannot get the system version of PCRE upgraded, you download and compile a local copy</span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="markdown">cd ~/src/</span>
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<td class="diff-line-num old old_line" data-linenumber="160" 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="LC160" class="line" lang="markdown">wget ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.41.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="markdown">tar zxvf pcre-8.41.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="markdown">cd pcre-8.41/</span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="markdown">./configure</span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="markdown">make</span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="markdown">Then pass that path to mosdepth just like we did with htslib</span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="markdown">LD_LIBRARY_PATH=~/src/pcre-8.41/.libs/:/~/src/htslib/ mosdepth -h</span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="markdown">If you still see an error about <span class="sb" style="color: #d14;">`could not import: pcre_free_study`</span> then </span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="markdown">for some, the solution has been to do: <span class="sb" style="color: #d14;">`ln -s /usr/local/lib/libpcre.so /usr/local/lib/libpcre.so.3`</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="markdown">If you do want to install from source, see the <span class="p">[</span><span class="nv" style="color: #008080;">travis.yml</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/mosdepth/blob/master/.travis.yml</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="markdown">and the <span class="p">[</span><span class="nv" style="color: #008080;">install.sh</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/mosdepth/blob/master/scripts/install.sh</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC175" 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">@@ -187,7 +185,7 @@ for at least a given coverage value. It does this for each chromosome, and for t</td>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown">whole genome.</span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="markdown">Each row will indicate:</span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="markdown"><span class="p"> +</span> chromosome (or "<span class="idiff left right">genome</span>")</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"><span class="p"> +</span> chromosome (or "<span class="idiff left right">total</span>")</span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="markdown"><span class="p"> +</span> coverage level</span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="markdown"><span class="p"> +</span> proportion of bases covered at that level</span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#98f5d7ecd16412a1f8781d3d8c896dd0323a69af"><strong>depthstat.nim</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="nim"><span class="k" style="font-weight: 600;">type</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="nim"> <span class="n" style="color: #333;">depth_stat</span><span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">object</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="nim"> <span class="n" style="color: #333;">cum_length</span><span class="o" style="font-weight: 600;">*</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="nim"> <span class="n" style="color: #333;">cum_depth</span><span class="o" style="font-weight: 600;">*</span><span class="p">:</span> <span class="n" style="color: #333;">uint64</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="nim"> <span class="n" style="color: #333;">min_depth</span><span class="o" style="font-weight: 600;">*</span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="nim"> <span class="n" style="color: #333;">max_depth</span><span class="o" style="font-weight: 600;">*</span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="nim"><span class="k" style="font-weight: 600;">type</span> <span class="n" style="color: #333;">CountStat</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333;">T</span><span class="p">:</span><span class="n" style="color: #333;">SomeOrdinal</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">object</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="nim"> <span class="n" style="color: #333;">counts</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="nim"> <span class="n" style="color: #333;">n</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">initCountStat</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">32768</span><span class="p">):</span> <span class="n" style="color: #333;">CountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">CountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">:</span> <span class="n" style="color: #333;">newSeq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">add</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">CountStat</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">T</span><span class="p">)</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">inc</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">inc</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="nim"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">value</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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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="nim"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">newException</span><span class="p">(</span><span class="n" style="color: #333;">IndexError</span><span class="p">,</span> <span class="s" style="color: #d14;">"error setting negative depth value:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">inc</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">median</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="n" style="color: #333;">CountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">stop_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="mf" style="color: #099;">0.5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">float64</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">cum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">cnt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="nim"> <span class="n" style="color: #333;">cum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cnt</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cum</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">stop_n</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">clear</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">CountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="nim"> <span class="n" style="color: #333;">zeroMem</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="k" style="font-weight: 600;">addr</span><span class="p">,</span> <span class="n" style="color: #333;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="nim"><span class="k" style="font-weight: 600;">template</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">:</span><span class="n" style="color: #333;">CountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">len</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">newDepthStat</span><span class="o" style="font-weight: 600;">*[</span><span class="n" style="color: #333;">T</span><span class="p">:</span> <span class="n" style="color: #333;">SomeNumber</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">]</span><span class="p">):</span> <span class="n" style="color: #333;">depth_stat</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">cum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">.</span><span class="n" style="color: #333;">high</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" 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="LC44" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">dp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">cum_depth</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dp</span><span class="p">.</span><span class="n" style="color: #333;">uint64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">dp</span><span class="p">.</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">max_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">max_depth</span><span class="p">,</span> <span class="n" style="color: #333;">dp</span><span class="p">.</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">clear</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">ds</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">depth_stat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="nim"> <span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">cum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="nim"> <span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">cum_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="nim"> <span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">.</span><span class="n" style="color: #333;">high</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="nim"> <span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">max_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">`+`</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="n" style="color: #333;">depth_stat</span><span class="p">):</span> <span class="n" style="color: #333;">depth_stat</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">depth_stat</span><span class="p">(</span><span class="n" style="color: #333;">cum_length</span><span class="p">:</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">cum_length</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">cum_length</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="nim"> <span class="n" style="color: #333;">cum_depth</span><span class="p">:</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">cum_depth</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">cum_depth</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="nim"> <span class="n" style="color: #333;">min_depth</span><span class="p">:</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="nim"> <span class="n" style="color: #333;">max_depth</span><span class="p">:</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">max_depth</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">max_depth</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="nim"><span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">isMainModule</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="nim"> <span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">unittest</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="nim"> <span class="n" style="color: #333;">suite</span> <span class="s" style="color: #d14;">"count-stat"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="nim"> <span class="n" style="color: #333;">test</span> <span class="s" style="color: #d14;">"count-test"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="nim"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initCountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">]</span><span class="p">()</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="mf" style="color: #099;">0</span><span class="p">..</span><span class="mi" style="color: #099;">10</span><span class="p">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="nim"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">11</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">32768</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="nim"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#5e05ccb32e2de6797c54768d95e4cc3ba8c8bc5f"><strong>functional-tests.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" 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">@@ -10,8 +10,10 @@ test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest</td>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-o</span> nounset</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell">nim c <span class="nt" style="color: #000080;">--boundChecks</span>:on <span class="nt" style="color: #000080;">-x</span>:on mosdepth.nim</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">nim c <span class="nt" style="color: #000080;">-r</span> tests/funcs.nim</span>
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15
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> +e</span>
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16
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">exe</span><span class="o" style="font-weight: 600;">=</span>./mosdepth</span>
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17
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">=</span>/data/human/NA12878.subset.bam</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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="28" 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">@@ -26,12 +28,16 @@ assert_exit_code 0</td>
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26
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zgrep ^MT t.per-base.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 0 80 1</span></span>
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27
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="s2" style="color: #d14;">MT 80 16569 0"</span></span>
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28
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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zgrep <span class="nt" style="color: #000080;">-w</span> ^1 t.per-base.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"1 0 249250621 0"</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'MT'</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 16569 80 0.00 0 1"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'total'</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"total 16569 80 0.00 0 1"</span></span>
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29
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"></span>
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30
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell">run overlapFastMode <span class="nv" style="color: #008080;">$exe</span> t <span class="nt" style="color: #000080;">--fast-mode</span> tests/ovl.bam</span>
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31
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zgrep ^MT t.per-base.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 0 6 1</span></span>
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32
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="s2" style="color: #d14;">MT 6 42 2</span></span>
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33
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="s2" style="color: #d14;">MT 42 80 1</span></span>
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34
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="s2" style="color: #d14;">MT 80 16569 0"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 2 | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span>+2 | <span class="nb" style="color: #0086b3;">sort</span> | <span class="nb" style="color: #0086b3;">uniq</span><span class="si" style="color: #d14;">)</span> 16569</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 4 | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span>+2 | <span class="nb" style="color: #0086b3;">sort</span> | <span class="nb" style="color: #0086b3;">uniq</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"0.01"</span></span>
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35
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell">assert_exit_code 0</span>
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36
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"></span>
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37
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" 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="47" 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">@@ -41,7 +47,7 @@ assert_exit_code 1</td>
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41
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell"></span>
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42
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell">run unordered_bed <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">--by</span> tests/unordered.bed t tests/ovl.bam</span>
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43
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell">assert_exit_code 0</span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span>zcat t.regions.bed.gz | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> 2</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span>zcat <span class="idiff left right">< </span>t.regions.bed.gz | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> 2</span>
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45
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"></span>
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46
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># theres data left in the bam but the region tree is empty...</span></span>
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47
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell">run missing_bed_chrom <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">--by</span> tests/missing.bed t tests/ovl.bam</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="74" 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">@@ -68,13 +74,13 @@ assert_exit_code 0</td>
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68
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"></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="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.thresholds.bed.gz<span class="k" style="font-weight: 600;">*</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="shell">run threshold_test <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">--by</span> 100 <span class="nt" style="color: #000080;">-T</span> 0,1,2,3,4,5 <span class="nt" style="color: #000080;">-c</span> MT t tests/ovl.bam</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat t.thresholds.bed.gz | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2 | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 0 100 unknown 100 80 0 0 0 0"</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"0"</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat t.thresholds.bed.gz | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span>+2 | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 7 | <span class="nb" style="color: #0086b3;">uniq</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat <span class="idiff left right">< </span>t.thresholds.bed.gz | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2 | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 0 100 unknown 100 80 0 0 0 0"</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"0"</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat <span class="idiff left right">< </span>t.thresholds.bed.gz | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span>+2 | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 7 | <span class="nb" style="color: #0086b3;">uniq</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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73
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell">assert_exit_code 0</span>
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74
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"></span>
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75
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.thresholds.bed.gz<span class="k" style="font-weight: 600;">*</span></span>
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76
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell">run threshold_test_by <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">--by</span> tests/track.bed <span class="nt" style="color: #000080;">-T</span> 0,1,2 <span class="nt" style="color: #000080;">-c</span> MT t tests/ovl.bam</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat t.thresholds.bed.gz | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 2 80 aregion 78 78 0"</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat <span class="idiff left right">< </span>t.thresholds.bed.gz | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 2 80 aregion 78 78 0"</span></span>
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78
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<td class="diff-line-num new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell">assert_exit_code 0</span>
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79
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"></span>
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80
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">MOSDEPTH_Q0</span><span class="o" style="font-weight: 600;">=</span>AAA</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" 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="91" 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">@@ -85,10 +91,13 @@ assert_exit_code 0</td>
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85
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zgrep <span class="nt" style="color: #000080;">-w</span> ^MT t.quantized.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 0 80 BBB</span></span>
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86
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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"><span class="s2" style="color: #d14;">MT 80 16569 AAA"</span></span>
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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span> t.mosdepth.global.dist.txt<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 1 0.0048283"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2 t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-1</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 16569 80 0.0048283 0 1"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> 1 t.mosdepth.summary.txt<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"total 16569 80 0.0048283 0 1"</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"></span>
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88
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="shell"></span>
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89
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="shell">run track_header <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">--by</span> tests/track.bed t tests/ovl.bam</span>
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90
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="shell">assert_exit_code 0</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat t.regions.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 2 80 aregion 1.00"</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat <span class="idiff left right">< </span>t.regions.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"MT 2 80 aregion 1.00"</span></span>
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92
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="shell"></span>
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93
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="shell">run track_header_by <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">--by</span> tests/bad.bed t tests/ovl.bam</span>
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94
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="shell">assert_exit_code 1</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">@@ -107,20 +116,38 @@ assert_equal "$(cat tt.mosdepth.global.dist.txt)" "MT 0 1.00</td>
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107
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"><span class="s2" style="color: #d14;">total 0 1.00"</span></span>
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108
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
109
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="shell">run big_chrom <span class="nv" style="color: #008080;">$exe</span> t tests/big.bam</span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> 3</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 3 | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2 | <span class="nb" style="color: #0086b3;">uniq</span><span class="si" style="color: #d14;">)</span> 15</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 5 | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2 | <span class="nb" style="color: #0086b3;">uniq</span><span class="si" style="color: #d14;">)</span> 0</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">cat </span>t.mosdepth.summary.txt | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 6 | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +2 | <span class="nb" style="color: #0086b3;">uniq</span><span class="si" style="color: #d14;">)</span> 1</span>
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110
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="shell">assert_exit_code 0</span>
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111
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="shell"></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> tt.mosdepth.region.dist.txt</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.mosdepth.region.dist.txt</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> tt.<span class="k" style="font-weight: 600;">*</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.<span class="k" style="font-weight: 600;">*</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"></span>
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114
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="shell">run empty_tids <span class="nv" style="color: #008080;">$exe</span> t <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">--thresholds</span> 1,5 <span class="nt" style="color: #000080;">--by</span> tests/empty-tids.bed tests/empty-tids.bam</span>
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115
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="shell">assert_exit_code 0</span>
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116
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-w</span> HPV26 <span class="nt" style="color: #000080;">-c</span> t.mosdepth.region.dist.txt<span class="si" style="color: #d14;">)</span> 0</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.<span class="k" style="font-weight: 600;">*</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#regions and global should not be the same when -b is specified</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="shell">run regions <span class="nv" style="color: #008080;">$exe</span> t_regions <span class="nt" style="color: #000080;">-n</span> <span class="nt" style="color: #000080;">-b</span> 100 tests/empty-tids.bam </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="shell">assert_equal <span class="si" style="color: #d14;">$(</span>diff <span class="nt" style="color: #000080;">-u</span> t_regions.mosdepth.region.dist.txt t_regions.mosdepth.global.dist.txt | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span> 1447</span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t_regions.<span class="k" style="font-weight: 600;">*</span></span>
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117
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<td class="diff-line-num new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.per-base.bed.gz<span class="k" style="font-weight: 600;">*</span></span>
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<td class="diff-line-num old_line" data-linenumber="119" 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">
119
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<td class="diff-line-num new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="shell">run overlappingPairs <span class="nv" style="color: #008080;">$exe</span> t tests/overlapping-pairs.bam</span>
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120
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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat t.per-base.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"1 0 565173 0</span></span>
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<td class="diff-line-num new old_line" data-linenumber="121" 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="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="shell">assert_equal <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span>zcat <span class="idiff left right">< </span>t.per-base.bed.gz<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"1 0 565173 0</span></span>
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<td class="diff-line-num old_line" data-linenumber="121" 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">
121
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<td class="diff-line-num new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="shell"><span class="s2" style="color: #d14;">1 565173 565253 1</span></span>
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<td class="diff-line-num old_line" data-linenumber="122" 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">
122
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<td class="diff-line-num new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="shell"><span class="s2" style="color: #d14;">1 565253 249250621 0"</span></span>
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<td class="diff-line-num old_line" data-linenumber="123" 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">
123
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<td class="diff-line-num new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="shell">assert_exit_code 0</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.<span class="k" style="font-weight: 600;">*</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="shell"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="shell"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="shell">nim c <span class="nt" style="color: #000080;">-d</span>:d4 <span class="nt" style="color: #000080;">--boundChecks</span>:on <span class="nt" style="color: #000080;">-x</span>:on mosdepth.nim</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> t.per-base.bed.gz</span>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="shell">run d4test <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">--d4</span> t <span class="nt" style="color: #000080;">--fast-mode</span> tests/ovl.bam</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="shell">assert_exit_code 0</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="shell"></span>
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124
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="shell"></span>
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125
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-e</span> <span class="nv" style="color: #008080;">$bam</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit</span></span>
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126
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -129,4 +156,13 @@ assert_equal "$(zgrep -w "chrM 9999 10000" t.per-base.bed.gz)" "chrM 9999 10000</td>
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129
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="shell">assert_exit_code 0</span>
</pre>
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130
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="131" 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">
131
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="shell">run flag <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">-c</span> chrM <span class="nt" style="color: #000080;">-F</span> 4 <span class="nt" style="color: #000080;">--by</span> 20000 tx /data/human/NA12878.subset.bam</span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="shell">assert_exit_code 0</span></pre>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="shell">assert_exit_code 0</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="shell"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="shell"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="shell">run check_exit_code_on_bad_args <span class="nv" style="color: #008080;">$exe</span> <span class="nt" style="color: #000080;">-t4prefix</span> sample.bam</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="shell">assert_exit_code 1</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="shell">assert_in_stderr <span class="s2" style="color: #d14;">"error parsing arguments"</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="shell"></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="shell"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="shell"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#3a6852ca596d0b268c25ad8cb502054fb3405cac"><strong>int2str.nim</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bitops</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="nim"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="nim"><span class="c" style="color: #998; font-style: italic;">#[</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="nim"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="nim"><span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">intToStr</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">adpated</span> <span class="k" style="font-weight: 600;">from</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">:</span><span class="o" style="font-weight: 600;">//</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">miloyip</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">itoa</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">benchmark</span> <span class="n" style="color: #333;">countlut</span> <span class="k" style="font-weight: 600;">method</span><span class="p">.</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="nim"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="nim"><span class="n" style="color: #333;">https</span><span class="p">:</span><span class="o" style="font-weight: 600;">//</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">miloyip</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">itoa</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">benchmark</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">blob</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">master</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">license</span><span class="p">.</span><span class="n" style="color: #333;">txt</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="nim"><span class="n" style="color: #333;">Copyright</span> <span class="p">(</span><span class="n" style="color: #333;">C</span><span class="p">)</span> <span class="mi" style="color: #099;">2014</span> <span class="n" style="color: #333;">Milo</span> <span class="n" style="color: #333;">Yip</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="nim"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="nim"><span class="n" style="color: #333;">Permission</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">hereby</span> <span class="n" style="color: #333;">granted</span><span class="p">,</span> <span class="n" style="color: #333;">free</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">charge</span><span class="p">,</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">person</span> <span class="n" style="color: #333;">obtaining</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">copy</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="nim"><span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">software</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">associated</span> <span class="n" style="color: #333;">documentation</span> <span class="n" style="color: #333;">files</span> <span class="p">(</span><span class="n" style="color: #333;">the</span> <span class="s" style="color: #d14;">"Software"</span><span class="p">),</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">deal</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="nim"><span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Software</span> <span class="k" style="font-weight: 600;">without</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">including</span> <span class="k" style="font-weight: 600;">without</span> <span class="n" style="color: #333;">limitation</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">rights</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="nim"><span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">use</span><span class="p">,</span> <span class="n" style="color: #333;">copy</span><span class="p">,</span> <span class="n" style="color: #333;">modify</span><span class="p">,</span> <span class="n" style="color: #333;">merge</span><span class="p">,</span> <span class="n" style="color: #333;">publish</span><span class="p">,</span> <span class="n" style="color: #333;">distribute</span><span class="p">,</span> <span class="n" style="color: #333;">sublicense</span><span class="p">,</span> <span class="ow" style="font-weight: 600;">and</span><span class="o" style="font-weight: 600;">/</span><span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sell</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="nim"><span class="n" style="color: #333;">copies</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Software</span><span class="p">,</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">permit</span> <span class="n" style="color: #333;">persons</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">whom</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Software</span> <span class="ow" style="font-weight: 600;">is</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="nim"><span class="n" style="color: #333;">furnished</span> <span class="n" style="color: #333;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">so</span><span class="p">,</span> <span class="n" style="color: #333;">subject</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">conditions</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="nim"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">above</span> <span class="n" style="color: #333;">copyright</span> <span class="n" style="color: #333;">notice</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">permission</span> <span class="n" style="color: #333;">notice</span> <span class="n" style="color: #333;">shall</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">included</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="nim"><span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">copies</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">substantial</span> <span class="n" style="color: #333;">portions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">Software</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="nim"><span class="n" style="color: #333;">THE</span> <span class="n" style="color: #333;">SOFTWARE</span> <span class="n" style="color: #333;">IS</span> <span class="n" style="color: #333;">PROVIDED</span> <span class="s" style="color: #d14;">"AS IS"</span><span class="p">,</span> <span class="n" style="color: #333;">WITHOUT</span> <span class="n" style="color: #333;">WARRANTY</span> <span class="n" style="color: #333;">OF</span> <span class="n" style="color: #333;">ANY</span> <span class="n" style="color: #333;">KIND</span><span class="p">,</span> <span class="n" style="color: #333;">EXPRESS</span> <span class="n" style="color: #333;">OR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="nim"><span class="n" style="color: #333;">IMPLIED</span><span class="p">,</span> <span class="n" style="color: #333;">INCLUDING</span> <span class="n" style="color: #333;">BUT</span> <span class="n" style="color: #333;">NOT</span> <span class="n" style="color: #333;">LIMITED</span> <span class="n" style="color: #333;">TO</span> <span class="n" style="color: #333;">THE</span> <span class="n" style="color: #333;">WARRANTIES</span> <span class="n" style="color: #333;">OF</span> <span class="n" style="color: #333;">MERCHANTABILITY</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="nim"><span class="n" style="color: #333;">FITNESS</span> <span class="n" style="color: #333;">FOR</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">PARTICULAR</span> <span class="n" style="color: #333;">PURPOSE</span> <span class="n" style="color: #333;">AND</span> <span class="n" style="color: #333;">NONINFRINGEMENT</span><span class="p">.</span> <span class="n" style="color: #333;">IN</span> <span class="n" style="color: #333;">NO</span> <span class="n" style="color: #333;">EVENT</span> <span class="n" style="color: #333;">SHALL</span> <span class="n" style="color: #333;">THE</span></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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="nim"><span class="n" style="color: #333;">AUTHORS</span> <span class="n" style="color: #333;">OR</span> <span class="n" style="color: #333;">COPYRIGHT</span> <span class="n" style="color: #333;">HOLDERS</span> <span class="n" style="color: #333;">BE</span> <span class="n" style="color: #333;">LIABLE</span> <span class="n" style="color: #333;">FOR</span> <span class="n" style="color: #333;">ANY</span> <span class="n" style="color: #333;">CLAIM</span><span class="p">,</span> <span class="n" style="color: #333;">DAMAGES</span> <span class="n" style="color: #333;">OR</span> <span class="n" style="color: #333;">OTHER</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="nim"><span class="n" style="color: #333;">LIABILITY</span><span class="p">,</span> <span class="n" style="color: #333;">WHETHER</span> <span class="n" style="color: #333;">IN</span> <span class="n" style="color: #333;">AN</span> <span class="n" style="color: #333;">ACTION</span> <span class="n" style="color: #333;">OF</span> <span class="n" style="color: #333;">CONTRACT</span><span class="p">,</span> <span class="n" style="color: #333;">TORT</span> <span class="n" style="color: #333;">OR</span> <span class="n" style="color: #333;">OTHERWISE</span><span class="p">,</span> <span class="n" style="color: #333;">ARISING</span> <span class="n" style="color: #333;">FROM</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="nim"><span class="n" style="color: #333;">OUT</span> <span class="n" style="color: #333;">OF</span> <span class="n" style="color: #333;">OR</span> <span class="n" style="color: #333;">IN</span> <span class="n" style="color: #333;">CONNECTION</span> <span class="n" style="color: #333;">WITH</span> <span class="n" style="color: #333;">THE</span> <span class="n" style="color: #333;">SOFTWARE</span> <span class="n" style="color: #333;">OR</span> <span class="n" style="color: #333;">THE</span> <span class="n" style="color: #333;">USE</span> <span class="n" style="color: #333;">OR</span> <span class="n" style="color: #333;">OTHER</span> <span class="n" style="color: #333;">DEALINGS</span> <span class="n" style="color: #333;">IN</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="nim"><span class="n" style="color: #333;">THE</span> <span class="n" style="color: #333;">SOFTWARE</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="nim"><span class="o" style="font-weight: 600;">]</span><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="nim"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gDigitsLut</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">[</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="nim"> <span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="nim"> <span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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="LC33" class="line" lang="nim"> <span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="nim"> <span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="35" 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="LC35" class="line" lang="nim"> <span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="nim"> <span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="nim"> <span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="nim"> <span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="nim"> <span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="nim"> <span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'0'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'1'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'2'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'3'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'4'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'5'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'6'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'7'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'8'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span><span class="p">,</span><span class="sc" style="color: #d14;">'9'</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="nim"><span class="o" style="font-weight: 600;">]</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="nim"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">powers_of_10</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">[</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="nim"> <span class="mi" style="color: #099;">0</span><span class="il" style="color: #099;">'i32</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="nim"> <span class="mi" style="color: #099;">10</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="nim"> <span class="mi" style="color: #099;">100</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="nim"> <span class="mi" style="color: #099;">1000</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="nim"> <span class="mi" style="color: #099;">10000</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="nim"> <span class="mi" style="color: #099;">100000</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="nim"> <span class="mi" style="color: #099;">1000000</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="nim"> <span class="mi" style="color: #099;">10000000</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="nim"> <span class="mi" style="color: #099;">100000000</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="nim"> <span class="mi" style="color: #099;">1000000000</span><span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">countdigits</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">countLeadingZeroBits</span><span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1233</span> <span class="ow" style="font-weight: 600;">shr</span> <span class="mi" style="color: #099;">12</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">-</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">powers_of_10</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">fastIntToStr</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">,</span> <span class="n" style="color: #333;">outstr</span><span class="p">:</span><span class="k" style="font-weight: 600;">var</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int</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 class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="nim"> <span class="n" style="color: #333;">outstr</span><span class="p">.</span><span class="n" style="color: #333;">setLen</span><span class="p">(</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">countdigits</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outstr</span><span class="p">.</span><span class="n" style="color: #333;">high</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="nim"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">100</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" 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">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">mod</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">shl</span> <span class="mi" style="color: #099;">1</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="nim"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="nim"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="nim"> <span class="n" style="color: #333;">outstr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">L</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gDigitsLut</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="nim"> <span class="n" style="color: #333;">outstr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">L</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gDigitsLut</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="nim"> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="nim"> <span class="n" style="color: #333;">outstr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">L</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">+</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">).</span><span class="kt" style="color: #458; font-weight: 600;">char</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="nim"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</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="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">shl</span> <span class="mi" style="color: #099;">1</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="nim"> <span class="n" style="color: #333;">outstr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">L</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gDigitsLut</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="nim"> <span class="n" style="color: #333;">outstr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">L</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gDigitsLut</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="nim"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="nim"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="nim"><span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">isMainModule</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="nim"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="nim"> <span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">times</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="nim"> <span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">strutils</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="nim"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpuTime</span><span class="p">()</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">outstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newString</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="mi" style="color: #099;">0</span><span class="il" style="color: #099;">'i32</span><span class="p">..</span><span class="mi" style="color: #099;">200_000_000</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="nim"> <span class="n" style="color: #333;">fastIntToStr</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">outstr</span><span class="p">)</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">outstr</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">i</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="n" style="color: #333;">cpuTime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t0</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="nim"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="nim"> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cpuTime</span><span class="p">()</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="s" style="color: #d14;">"only to 100m for $"</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="mi" style="color: #099;">0</span><span class="il" style="color: #099;">'i32</span><span class="p">..</span><span class="mi" style="color: #099;">100_000_000</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">outstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="n" style="color: #333;">cpuTime</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t0</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">hts</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tables</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="p">.</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">int2str</span></span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">strutils</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">S</span></span>
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4
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">algorithm</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">alg</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sequtils</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">sequtils</span></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">strutils</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">su</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">strformat</span></span>
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8
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">docopt</span></span>
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9
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">times</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">math</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="p">.</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">depthstat</span></span>
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10
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="nim"><span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="nim"> <span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">d4</span></span>
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11
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="nim"></span>
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12
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">precision</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">output_summary_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">true</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="nim"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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14
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getEnv</span><span class="p">(</span><span class="s" style="color: #d14;">"MOSDEPTH_PRECISION"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="nim"> <span class="n" style="color: #333;">precision</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="28" 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">@@ -20,11 +28,11 @@ type</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="nim"> <span class="n" style="color: #333;">pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">tuple</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pos</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="nim"> <span class="n" style="color: #333;">depth_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">tuple</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">start</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="nim"> <span class="n" style="color: #333;">depth_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">tuple</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">start</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="nim"> <span class="n" style="color: #333;">region_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">ref</span> <span class="k" style="font-weight: 600;">object</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="nim"> <span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="nim"> <span class="n" style="color: #333;">start</span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="nim"> <span class="n" style="color: #333;">stop</span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="nim"> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="nim"> <span class="n" style="color: #333;">region_t</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">ref</span> <span class="k" style="font-weight: 600;">object</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="nim"> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="nim"> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="nim"> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="nim"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="nim"> <span class="n" style="color: #333;">coverage_t</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="nim"></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">@@ -38,10 +46,7 @@ proc `$`*(r: region_t): string =</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">to_coverage</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">coverage_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># to_coverage converts from an array of start/end inc/decs to actual coverage.</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pairs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="nim"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">v</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="nim"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">cumsum</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="nim"><span class="k" style="font-weight: 600;">iterator</span> <span class="n" style="color: #333;">gen_depths</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">:</span> <span class="n" style="color: #333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">istop</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">):</span> <span class="n" style="color: #333;">depth_t</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># given `arr` with values in each index indicating the number of reads</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">@@ -125,7 +130,7 @@ iterator gen_quantized(quants: seq[int], arr: coverage_t): depth_s {.inline.} =</td>
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125
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="nim"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">last_pos</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">last_quantized</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="nim"> <span class="n" style="color: #333;">last_quantized</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quantized</span></span>
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127
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="nim"> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_quantized</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">arr</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last_quantized</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">arr</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">last_quantized</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">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lookup</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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129
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="nim"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">last_pos</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">lookup</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">last_quantized</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="nim"></span>
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131
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">pair_sort</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">:</span> <span class="n" style="color: #333;">pair</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" 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="189" 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">@@ -184,24 +189,28 @@ proc bed_line_to_region(line: string): region_t =</td>
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184
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="nim"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">cse</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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185
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="nim"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">cse</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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186
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="nim"> <span class="n" style="color: #333;">reg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region_t</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="n" style="color: #333;">cse</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">stop</span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"[slivar] ERROR: start > end in bed line:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">line</span></span>
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187
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">cse</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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188
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="nim"> <span class="n" style="color: #333;">reg</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cse</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">]</span></span>
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189
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reg</span></span>
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190
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="nim"></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">region_line_to_region</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">):</span> <span class="n" style="color: #333;">region_t</span> <span class="o" style="font-weight: 600;">=</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">region_line_to_region</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">):</span> <span class="n" style="color: #333;">region_t</span> <span class="o" style="font-weight: 600;">=</span></span>
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192
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<td class="diff-line-num new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">region</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">region</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"nil"</span><span class="p">:</span></span>
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193
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<td class="diff-line-num new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">nil</span></span>
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<td class="diff-line-num new new_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="sc" style="color: #d14;">':'</span> <span class="ow" style="font-weight: 600;">notin</span> <span class="n" style="color: #333;">region</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">region_t</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">:</span><span class="n" style="color: #333;">region</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region_t</span><span class="p">()</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="nim"></span>
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194
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="nim"> <span class="k" style="font-weight: 600;"><span class="idiff left">var</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">r</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">region_t</span></span><span class="p"><span class="idiff right">()</span></span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">region</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">split</span></span><span class="p"><span class="idiff">({</span></span><span class="sc" style="color: #d14;"><span class="idiff">':'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'-'</span></span><span class="p"><span class="idiff right">}</span>):</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># rsplit yields strings in reverse order</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="206" 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">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">region</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">rsplit</span></span><span class="p"><span class="idiff">({</span></span><span class="sc" style="color: #d14;"><span class="idiff">':'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'-'</span></span><span class="p"><span class="idiff">},</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxsplit</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">):</span></span>
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197
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<td class="diff-line-num new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="nim"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num old old_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="nim"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">:</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="nim"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="nim"> <span class="n" style="color: #333;">r<span class="idiff left right">esult</span></span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="nim"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">:</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="nim"> <span class="n" style="color: #333;">r<span class="idiff left right">esult</span></span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">))</span></span>
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201
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="nim"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="nim"> <span class="n" style="color: #333;">r<span class="idiff left right">esult</span></span><span class="p">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span></span>
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203
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="nim"> <span class="n" style="color: #333;">inc</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span></span>
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205
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="nim"></span>
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206
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">get_tid</span><span class="p">(</span><span class="n" style="color: #333;">tgts</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hts</span><span class="p">.</span><span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span></span>
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207
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tgts</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="285" 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>
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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">@@ -285,11 +294,10 @@ proc coverage(bam: hts.Bam, arr: var coverage_t, region: var region_t, mapq:int=</td>
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285
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># 4623241 4623264</span></span>
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286
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># chr1 4623171 69M1D23M9S (pos: 4623171, value: 1)(pos: 4623241, value: 1)(pos: 4623240, value: -1)(pos: 4623264, value: -1)</span></span>
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287
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># chr1 4623223 4S97M (pos: 4623223, value: 1)(pos: 4623320, value: -1)</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="nim"> <span class="n" style="color: #333;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># each element will have a .value of 1 for start and -1 for end.</span></span>
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290
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="nim"></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">ses</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequtils</span><span class="p">.</span><span class="n" style="color: #333;">to_seq</span><span class="p">(</span><span class="n" style="color: #333;">gen_start_ends</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">))</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gen_start_ends</span><span class="p">(</span><span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">ses</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequtils</span><span class="p">.</span><span class="n" style="color: #333;">to_seq</span><span class="p">(</span><span class="n" style="color: #333;">gen_start_ends</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p"><span class="idiff left">.</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gen_start_ends</span><span class="p">(</span><span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p"><span class="idiff left">.</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span><span class="p">):</span></span>
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293
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<td class="diff-line-num new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="nim"> <span class="n" style="color: #333;">ses</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="294" 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">
294
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<td class="diff-line-num new_line" data-linenumber="302" 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">
302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="nim"> <span class="n" style="color: #333;">alg</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">ses</span><span class="p">,</span> <span class="n" style="color: #333;">pair_sort</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="295" 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">
295
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<td class="diff-line-num new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">pair_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="306" 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="314" 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">@@ -306,10 +314,10 @@ proc coverage(bam: hts.Bam, arr: var coverage_t, region: var region_t, mapq:int=</td>
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306
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<td class="diff-line-num new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="nim"> <span class="n" style="color: #333;">last_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">pos</span></span>
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307
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<td class="diff-line-num new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pair_depth</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">echo</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">qname</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">rec</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="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">mate</span><span class="p">.</span><span class="n" style="color: #333;">qname</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">mate</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="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">pair_depth</span></span>
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<td class="diff-line-num old_line" data-linenumber="308" 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">
308
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<td class="diff-line-num new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fast_mode</span><span class="p">:</span></span>
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309
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<td class="diff-line-num new_line old" data-linenumber="317" 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="LC309" class="line" lang="nim"> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">]</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">inc</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="310" 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">
310
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<td class="diff-line-num new_line old" data-linenumber="317" 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="LC310" class="line" lang="nim"> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">]</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">dec</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="317" 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">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="nim"> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">]</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="nim"> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">]</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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311
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<td class="diff-line-num new_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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312
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<td class="diff-line-num new_line old" data-linenumber="320" 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="LC312" class="line" lang="nim"> <span class="n" style="color: #333;">inc_coverage</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">arr</span><span class="p">)</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="nim"> <span class="n" style="color: #333;">inc_coverage</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p"><span class="idiff left">.</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int</span></span><span class="p">,</span> <span class="n" style="color: #333;">arr</span><span class="p">)</span></span>
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313
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<td class="diff-line-num new_line" data-linenumber="321" 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">
321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="nim"></span>
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314
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<td class="diff-line-num new_line" data-linenumber="322" 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">
322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">found</span><span class="p">:</span></span>
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315
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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">@@ -352,28 +360,33 @@ iterator region_gen(window: uint32, target: hts.Target, bed_regions: TableRef[st</td>
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352
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bed_regions</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">]</span><span class="p">:</span> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">r</span></span>
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353
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="nim"> <span class="n" style="color: #333;">bed_regions</span><span class="p">.</span><span class="n" style="color: #333;">del</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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354
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="nim"></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">imean</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">:</span> <span class="n" style="color: #333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span> <span class="o" style="font-weight: 600;">=</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">imean</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">:</span> <span class="n" style="color: #333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ms</span></span><span class="p"><span class="idiff">:</span></span><span class="k" style="font-weight: 600;"><span class="idiff">var</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CountStat</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">uint32</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span></span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span> <span class="o" style="font-weight: 600;">=</span></span>
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356
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">)):</span></span>
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357
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">)</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">start</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">stop</span><span class="p">:</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">):</span> <span class="k" style="font-weight: 600;">break</span></span>
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361
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<td class="diff-line-num new_line old" data-linenumber="366" 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="LC361" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">+=</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">L</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="nim"></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ms</span><span class="p">.</span><span class="n" style="color: #333;">len</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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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="nim"> <span class="n" style="color: #333;">ms</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">()</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">start</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">))):</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="nim"> <span class="n" style="color: #333;">ms</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="371" 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">
371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ms</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">float64</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="nim"></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="375" 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">
375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">start</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">))):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="376" 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">
376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">+=</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">L</span></span>
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362
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="nim"></span>
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363
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<td class="diff-line-num new_line" data-linenumber="378" 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">
378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="nim"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">MAX_COVERAGE</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">(</span><span class="mi" style="color: #099;">400000</span><span class="p">)</span></span>
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364
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<td class="diff-line-num new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="nim"></span>
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365
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<td class="diff-line-num new_line old" data-linenumber="380" 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="LC365" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">inc</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">:</span> <span class="n" style="color: #333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num new old_line" data-linenumber="366" 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="380" 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">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">inc</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">coverage</span><span class="p">:</span> <span class="k" style="font-weight: 600;"><span class="idiff left">var</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">:</span><span class="n" style="color: #333;">uint32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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366
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">v</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int32</span></span>
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367
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="p">)</span></span>
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368
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<td class="diff-line-num new_line" data-linenumber="383" 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">
383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="p">):</span></span>
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369
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<td class="diff-line-num new_line" data-linenumber="384" 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">
384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span><span class="p">(</span><span class="s" style="color: #d14;">"[mosdepth] warning requested interval outside of chromosome range:"</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="s" style="color: #d14;">".."</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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370
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<td class="diff-line-num new_line" data-linenumber="385" 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">
385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span></span>
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371
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<td class="diff-line-num new_line old" data-linenumber="386" 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="LC371" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">istop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stop</span></span>
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372
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<td class="diff-line-num new_line old" data-linenumber="386" 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="LC372" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="p">):</span></span>
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373
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<td class="diff-line-num new_line old" data-linenumber="386" 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="LC373" class="line" lang="nim"> <span class="n" style="color: #333;">istop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">istop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">))</span></span>
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374
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="nim"></span>
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375
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">start</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">istop</span><span class="p">:</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="nim"> <span class="n" style="color: #333;">v</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="kt" style="color: #458; font-weight: 600;">i<span class="idiff left">nt</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">)</span></span><span class="o" style="font-weight: 600;">]</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="nim"> <span class="n" style="color: #333;">v</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="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span></span>
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377
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">MAX_COVERAGE</span><span class="p">:</span></span>
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378
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="nim"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX_COVERAGE</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">10</span></span>
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379
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">L</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="382" 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="395" 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">@@ -382,7 +395,7 @@ proc inc(d: var seq[int64], coverage: coverage_t, start:uint32, stop:uint32) =</td>
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382
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="nim"> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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383
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="nim"> <span class="n" style="color: #333;">L</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="p">)</span></span>
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384
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="nim"> <span class="n" style="color: #333;"><span class="idiff left">inc</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="p"><span class="idiff right">)</span></span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="nim"> <span class="n" style="color: #333;"><span class="idiff left">d</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">v</span></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="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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386
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="nim"></span>
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387
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">write_distribution</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span><span class="n" style="color: #333;">File</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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388
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">sum</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int64</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="404" 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="417" 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">@@ -404,6 +417,28 @@ proc write_distribution(chrom: string, d: var seq[int64], fh:File) =</td>
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404
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># reverse it back because we use to update the full genome</span></span>
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405
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="nim"> <span class="n" style="color: #333;">reverse</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>
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406
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">write_summary</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">stat</span><span class="p">:</span> <span class="n" style="color: #333;">depth_stat</span><span class="p">,</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span><span class="n" style="color: #333;">File</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">mean_depth</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="422" 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">
422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">cum_length</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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<td class="diff-line-num new new_line" data-linenumber="423" 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">
423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="nim"> <span class="n" style="color: #333;">mean_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">cum_depth</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="kt" style="color: #458; font-weight: 600;">float64</span><span class="p">(</span><span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">cum_length</span><span class="p">)</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="nim"> <span class="n" style="color: #333;">mean_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="kt" style="color: #458; font-weight: 600;">float64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="426" 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">
426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">stat_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">uint32</span><span class="p">.</span><span class="n" style="color: #333;">high</span><span class="p">:</span> <span class="mf" style="color: #099;">0.</span><span class="n" style="color: #333;">uint32</span> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">min_depth</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">output_summary_header</span><span class="p">:</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="nim"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span> <span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">,</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="nim"> <span class="s" style="color: #d14;">"length"</span><span class="p">,</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="nim"> <span class="s" style="color: #d14;">"bases"</span><span class="p">,</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="nim"> <span class="s" style="color: #d14;">"mean"</span><span class="p">,</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="nim"> <span class="s" style="color: #d14;">"min"</span><span class="p">,</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="nim"> <span class="s" style="color: #d14;">"max"</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="434" 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">
434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="nim"> <span class="n" style="color: #333;">output_summary_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">false</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="nim"> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span> <span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">region</span><span class="p">,</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="nim"> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">cum_length</span><span class="p">,</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="nim"> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">cum_depth</span><span class="p">,</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="nim"> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">mean_depth</span><span class="p">.</span><span class="n" style="color: #333;">format_float</span><span class="p">(</span><span class="n" style="color: #333;">ffDecimal</span><span class="p">,</span> <span class="n" style="color: #333;">precision</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">precision</span><span class="p">),</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="nim"> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">stat_min</span><span class="p">,</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="nim"> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">stat</span><span class="p">.</span><span class="n" style="color: #333;">max_depth</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="nim"></span>
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407
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442
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">get_targets</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hts</span><span class="p">.</span><span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">:</span> <span class="n" style="color: #333;">region_t</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hts</span><span class="p">.</span><span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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409
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">targets</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">@@ -444,11 +479,11 @@ proc get_quantize_args*(qa: string) : seq[int] =</td>
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479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="nim"> <span class="n" style="color: #333;">quit</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="nim"></span>
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="nim"></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">write_thresholds</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">:</span><span class="n" style="color: #333;">BGZI</span><span class="p">,</span> <span class="n" style="color: #333;">tid</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">arr</span><span class="p">:</span><span class="n" style="color: #333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333;">thresholds</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="n" style="color: #333;">region_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">write_thresholds</span><span class="p">(</span><span class="n" style="color: #333;">fh</span><span class="p">:</span><span class="n" style="color: #333;">BGZI</span><span class="p">,</span> <span class="n" style="color: #333;">tid</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">arr</span><span class="p">:</span><span class="k" style="font-weight: 600;"><span class="idiff left">var</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">coverage_t</span><span class="p">,</span> <span class="n" style="color: #333;">thresholds</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="n" style="color: #333;">region_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># write the number of bases in each region that are >= each threshold.</span></span>
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">thresholds</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="nim"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_string_of_cap</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="nim"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_string_of_cap</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">32</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="nim"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="nim"> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="nim"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</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">@@ -466,13 +501,14 @@ proc write_thresholds(fh:BGZI, tid:int, arr:coverage_t, thresholds:seq[int], reg</td>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">thresholds</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="nim"> <span class="n" style="color: #333;">shallow</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># iterate over the region and count bases >= request cutoffs.</span></span>
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">start</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">]</span><span class="p">:</span></span>
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">thresholds</span><span class="p">:</span></span>
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473
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="nim"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">v</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">t</span></span><span class="p"><span class="idiff right">:</span></span></span>
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474
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="nim"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">counts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></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="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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475
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># else: break # if we know they are sorted we can break</span></span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># if we know they are sorted we can break</span></span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="nim"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">v</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">t</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">break</span></span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="nim"> <span class="n" style="color: #333;"><span class="idiff left">counts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></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="mi" style="color: #099;"><span class="idiff right">1</span></span></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">counts</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="nim"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="n" style="color: #333;">count</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">@@ -498,8 +534,18 @@ proc get_min_levels(targets: seq[Target]): int =</td>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="nim"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">shl</span> <span class="mi" style="color: #099;">3</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">isdigit</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">s</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">isdigit</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">false</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">true</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="nim"></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">to_tuples</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">]</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="k" style="font-weight: 600;">tuple</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">name</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]]</span> <span class="o" style="font-weight: 600;">=</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">setLen</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">targets</span><span class="p">:</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="nim"></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">:</span> <span class="n" style="color: #333;">hts</span><span class="p">.</span><span class="n" style="color: #333;">Bam</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="n" style="color: #333;">region_t</span><span class="p">,</span> <span class="n" style="color: #333;">mapq</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">eflag</span><span class="p">:</span> <span class="n" style="color: #333;">uint16</span><span class="p">,</span> <span class="n" style="color: #333;">iflag</span><span class="p">:</span> <span class="n" style="color: #333;">uint16</span><span class="p">,</span> <span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">thresholds</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">fast_mode</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">:</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">docopt</span><span class="p">.</span><span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">:</span> <span class="n" style="color: #333;">hts</span><span class="p">.</span><span class="n" style="color: #333;">Bam</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="n" style="color: #333;">region_t</span><span class="p">,</span> <span class="n" style="color: #333;">mapq</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">eflag</span><span class="p">:</span> <span class="n" style="color: #333;">uint16</span><span class="p">,</span> <span class="n" style="color: #333;">iflag</span><span class="p">:</span> <span class="n" style="color: #333;">uint16</span><span class="p">,</span> <span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">thresholds</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="nim"> <span class="n" style="color: #333;">fast_mode</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">:</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">docopt</span><span class="p">.</span><span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">use_median</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="kp" style="font-weight: 600;">false</span><span class="p">,</span> <span class="n" style="color: #333;">use_d4</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="kp" style="font-weight: 600;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># windows are either from regions, or fixed-length windows.</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># we assume the input is sorted by chrom.</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</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">@@ -512,15 +558,25 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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512
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="nim"> <span class="n" style="color: #333;">skip_per_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--no-per-base"</span><span class="o" style="font-weight: 600;">]</span></span>
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513
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="nim"> <span class="n" style="color: #333;">window</span><span class="p">:</span> <span class="n" style="color: #333;">uint32</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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514
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="nim"> <span class="n" style="color: #333;">bed_regions</span><span class="p">:</span> <span class="n" style="color: #333;">TableRef</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">region_t</span><span class="o" style="font-weight: 600;">]]</span> <span class="c" style="color: #998; font-style: italic;"># = Table[string, seq[region_t]]</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="nim"> <span class="n" style="color: #333;">fbase</span><span class="p">:</span> <span class="n" style="color: #333;">BGZI</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;">#fbase: BGZ</span></span>
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="nim"> <span class="n" style="color: #333;">fquantize</span><span class="p">:</span> <span class="n" style="color: #333;">BGZI</span></span>
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="nim"> <span class="n" style="color: #333;">fthresholds</span><span class="p">:</span> <span class="n" style="color: #333;">BGZI</span></span>
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519
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="nim"> <span class="n" style="color: #333;">fregion</span><span class="p">:</span> <span class="n" style="color: #333;">BGZI</span></span>
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520
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="nim"> <span class="n" style="color: #333;">fh_global_dist</span><span class="p">:</span><span class="n" style="color: #333;">File</span></span>
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521
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="nim"> <span class="n" style="color: #333;">fh_region_dist</span><span class="p">:</span><span class="n" style="color: #333;">File</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="nim"> <span class="n" style="color: #333;">fh_summary</span><span class="p">:</span> <span class="n" style="color: #333;">File</span></span>
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522
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="nim"> <span class="n" style="color: #333;">quantize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_quantize_args</span><span class="p">(</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--quantize"</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># summary stat output</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_region_stat</span><span class="p">:</span> <span class="n" style="color: #333;">depth_stat</span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_stat</span><span class="p">:</span> <span class="n" style="color: #333;">depth_stat</span></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="nim"> <span class="n" style="color: #333;">global_region_stat</span><span class="p">:</span> <span class="n" style="color: #333;">depth_stat</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="nim"> <span class="n" style="color: #333;">global_stat</span><span class="p">:</span> <span class="n" style="color: #333;">depth_stat</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="nim"></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fd4</span><span class="p">:</span><span class="n" style="color: #333;">D4</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fbase</span><span class="p">:</span> <span class="n" style="color: #333;">BGZI</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="nim"></span>
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524
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<td class="diff-line-num new_line" data-linenumber="580" 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">
580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">region_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>
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525
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<td class="diff-line-num new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">global_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>
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526
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="nim"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="590" 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">@@ -534,7 +590,13 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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534
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<td class="diff-line-num new_line" data-linenumber="590" 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">
590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">skip_per_base</span><span class="p">:</span></span>
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535
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<td class="diff-line-num new_line" data-linenumber="591" 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">
591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># can't use set-threads when indexing on the fly so this must</span></span>
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536
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<td class="diff-line-num new_line" data-linenumber="592" 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">
592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># not call set_threads().</span></span>
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537
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<td class="diff-line-num new_line old" data-linenumber="593" 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="LC537" class="line" lang="nim"> <span class="n" style="color: #333;">fbase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wopen_bgzi</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".per-base.bed.gz"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="kp" style="font-weight: 600;">true</span><span class="p">,</span> <span class="n" style="color: #333;">compression_level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">levels</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">levels</span><span class="p">)</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_d4</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" 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">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">fd4</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".per-base.d4"</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="s" style="color: #d14;">"[mosdepth] error opening {prefix}.per-base.d4"</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="nim"> <span class="n" style="color: #333;">fd4</span><span class="p">.</span><span class="n" style="color: #333;">set_chromosomes</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">to_tuples</span><span class="p">)</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="598" 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">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="599" 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">
599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="nim"> <span class="n" style="color: #333;">fbase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wopen_bgzi</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".per-base.bed.gz"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="kp" style="font-weight: 600;">true</span><span class="p">,</span> <span class="n" style="color: #333;">compression_level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">levels</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">levels</span><span class="p">)</span></span>
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538
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;">#open(fbase, prefix & ".per-base.bed.gz", "w1")</span></span>
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539
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<td class="diff-line-num new_line" data-linenumber="601" 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">
601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">quantize</span><span class="p">.</span><span class="n" style="color: #333;">len</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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540
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602
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="nim"> <span class="n" style="color: #333;">fquantize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wopen_bgzi</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".quantized.bed.gz"</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="kp" style="font-weight: 600;">true</span><span class="p">,</span> <span class="n" style="color: #333;">compression_level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">levels</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">levels</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="546" 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="608" 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">@@ -546,6 +608,9 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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546
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<td class="diff-line-num new_line" data-linenumber="608" 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">
608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">fh_global_dist</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".mosdepth.global.dist.txt"</span><span class="p">,</span> <span class="n" style="color: #333;">fmWrite</span><span class="p">):</span></span>
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547
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<td class="diff-line-num new_line" data-linenumber="609" 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">
609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span><span class="p">(</span><span class="s" style="color: #d14;">"[mosdepth] could not open file:"</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".mosdepth.global.dist.txt"</span><span class="p">)</span></span>
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548
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="611" 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">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">fh_summary</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".mosdepth.summary.txt"</span><span class="p">,</span> <span class="n" style="color: #333;">fmWrite</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="612" 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">
612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span><span class="p">(</span><span class="s" style="color: #d14;">"[mosdepth] could not open file:"</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".mosdepth.summary.txt"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="613" 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">
613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="nim"></span>
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549
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<td class="diff-line-num new_line" data-linenumber="614" 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">
614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">region</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">fh_region_dist</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".mosdepth.region.dist.txt"</span><span class="p">,</span> <span class="n" style="color: #333;">fmWrite</span><span class="p">):</span></span>
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550
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<td class="diff-line-num new_line" data-linenumber="615" 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">
615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span><span class="p">(</span><span class="s" style="color: #d14;">"[mosdepth] could not open file:"</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">".mosdepth.dist.txt"</span><span class="p">)</span></span>
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551
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="nim"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="555" 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="620" 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">@@ -555,6 +620,9 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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555
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<td class="diff-line-num new_line" data-linenumber="620" 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">
620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="nim"> <span class="n" style="color: #333;">window</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="556" 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">
556
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<td class="diff-line-num new_line" data-linenumber="621" 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">
621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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557
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<td class="diff-line-num new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="nim"> <span class="n" style="color: #333;">bed_regions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bed_to_table</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="623" 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">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="nim"> <span class="n" style="color: #333;">shallow</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="624" 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">
624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="625" 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">
625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">cs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">initCountStat</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">uint32</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_median</span><span class="p">:</span> <span class="mi" style="color: #099;">65536</span> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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558
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<td class="diff-line-num new_line" data-linenumber="626" 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">
626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="nim"></span>
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<td class="diff-line-num old_line" data-linenumber="559" 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">
559
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<td class="diff-line-num new_line" data-linenumber="627" 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">
627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">target</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sub_targets</span><span class="p">:</span></span>
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560
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<td class="diff-line-num new_line" data-linenumber="628" 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">
628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_global_distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int64</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="575" 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="643" 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">@@ -575,7 +643,8 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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575
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<td class="diff-line-num new_line" data-linenumber="643" 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">
643
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0'f64</span></span>
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<td class="diff-line-num old_line" data-linenumber="576" 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">
576
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<td class="diff-line-num new_line" data-linenumber="644" 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">
644
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">region_gen</span><span class="p">(</span><span class="n" style="color: #333;">window</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">bed_regions</span><span class="p">):</span></span>
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<td class="diff-line-num old_line" data-linenumber="577" 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">
577
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<td class="diff-line-num new_line" data-linenumber="645" 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">
645
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="nim"> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">imean</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="nim"> <span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">imean</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">cs</span><span class="p">)</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_region_stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom_region_stat</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newDepthStat</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">su</span><span class="p">.</span><span class="n" style="color: #333;">format_float</span><span class="p">(</span><span class="n" style="color: #333;">me</span><span class="p">,</span> <span class="n" style="color: #333;">ffDecimal</span><span class="p">,</span> <span class="n" style="color: #333;">precision</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">precision</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</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="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="585" 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="654" 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">@@ -585,10 +654,21 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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585
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">fregion</span><span class="p">.</span><span class="n" style="color: #333;">write_interval</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">),</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">))</span></span>
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="nim"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">[</span><span class="mf" style="color: #099;">0</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span></span>
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_region_distribution</span><span class="p">.</span><span class="n" style="color: #333;">inc</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">region</span><span class="p">.</span><span class="n" style="color: #333;">isdigit</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;">#stores the aggregated coverage for each region when working with even windows across the genome</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_region_distribution</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">me</span><span class="p">.</span><span class="n" style="color: #333;">toInt</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int64</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">chrom_region_distribution</span><span class="p">))</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="659" 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="LC659" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;"># stores the per-base coverage in each region specified in the bed file</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_region_distribution</span><span class="p">.</span><span class="n" style="color: #333;">inc</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="nim"></span>
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589
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="nim"> <span class="n" style="color: #333;">write_thresholds</span><span class="p">(</span><span class="n" style="color: #333;">fthresholds</span><span class="p">,</span> <span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">thresholds</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">)</span></span>
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590
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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591
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_global_distribution</span><span class="p">.</span><span class="n" style="color: #333;">inc</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">uint32</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newDepthStat</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="o" style="font-weight: 600;">[</span><span class="mf" style="color: #099;">0</span><span class="p">..</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="nim"> <span class="n" style="color: #333;">global_stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_stat</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chrom_stat</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="nim"> <span class="n" style="color: #333;">write_summary</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_stat</span><span class="p">,</span> <span class="n" style="color: #333;">fh_summary</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="668" 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">
668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">region</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="nim"> <span class="n" style="color: #333;">write_summary</span><span class="p">(</span><span class="n" style="color: #333;">target</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;">"_region"</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_region_stat</span><span class="p">,</span> <span class="n" style="color: #333;">fh_summary</span><span class="p">)</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="nim"> <span class="n" style="color: #333;">global_region_stat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">global_region_stat</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chrom_region_stat</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="nim"> <span class="n" style="color: #333;">chrom_region_stat</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">()</span></span>
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592
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672
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="nim"></span>
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673
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># write the distribution for each chrom</span></span>
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594
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="nim"> <span class="n" style="color: #333;">write_distribution</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_global_distribution</span><span class="p">,</span> <span class="n" style="color: #333;">fh_global_dist</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="603" 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="683" 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">@@ -603,10 +683,30 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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603
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="nim"></span>
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604
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">skip_per_base</span><span class="p">:</span></span>
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605
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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606
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<td class="diff-line-num new_line old" data-linenumber="686" 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="LC606" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">fbase</span><span class="p">.</span><span class="n" style="color: #333;">write_interval</span><span class="p">(</span><span class="n" style="color: #333;">starget</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0"</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">))</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_d4</span><span class="p">:</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="nim"> <span class="n" style="color: #333;">fd4</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">@[</span><span class="n" style="color: #333;">Interval</span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">:</span> <span class="mi" style="color: #099;">0'u32</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">:</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">.</span><span class="n" style="color: #333;">uint32</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="il" style="color: #099;">'i32</span><span class="p">)</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="689" 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">
689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="690" 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">
690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">fbase</span><span class="p">.</span><span class="n" style="color: #333;">write_interval</span><span class="p">(</span><span class="n" style="color: #333;">starget</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0"</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">))</span></span>
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607
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<td class="diff-line-num new_line" data-linenumber="691" 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">
691
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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608
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<td class="diff-line-num new_line old" data-linenumber="692" 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="LC608" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gen_depths</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">):</span></span>
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609
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<td class="diff-line-num new_line old" data-linenumber="692" 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="LC609" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">fbase</span><span class="p">.</span><span class="n" style="color: #333;">write_interval</span><span class="p">(</span><span class="n" style="color: #333;">starget</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">),</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="692" 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">
692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">write_fbase</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num new new_line" data-linenumber="693" 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">
693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="694" 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">
694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_d4</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="695" 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">
695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="nim"> <span class="n" style="color: #333;">fd4</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">arr</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="696" 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">
696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="nim"> <span class="n" style="color: #333;">write_fbase</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">false</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="698" 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">
698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">write_fbase</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="699" 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">
699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newStringOfCap</span><span class="p">(</span><span class="mi" style="color: #099;">32</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="700" 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">
700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="nim"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">starget</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="701" 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">
701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gen_depths</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="702" 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">
702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># re-use line each time.</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="nim"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">setLen</span><span class="p">(</span><span class="n" style="color: #333;">starget</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="704" 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">
704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="nim"> <span class="n" style="color: #333;">fastIntToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="nim"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="sc" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="sc" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="706" 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">
706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="nim"> <span class="n" style="color: #333;">fastIntToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="707" 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">
707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="nim"> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="sc" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="sc" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="708" 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">
708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="nim"> <span class="n" style="color: #333;">fastIntToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="610" 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="709" 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">
709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">fbase</span><span class="p">.</span><span class="n" style="color: #333;">write_interval</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="610" 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">
610
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<td class="diff-line-num new_line" data-linenumber="710" 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">
710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">quantize</span><span class="p">.</span><span class="n" style="color: #333;">len</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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<td class="diff-line-num old_line" data-linenumber="611" 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">
611
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<td class="diff-line-num new_line" data-linenumber="711" 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">
711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">quantize</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</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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<td class="diff-line-num old_line" data-linenumber="612" 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">
612
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<td class="diff-line-num new_line" data-linenumber="712" 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">
712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">lookup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_lookup</span><span class="p">(</span><span class="n" style="color: #333;">quantize</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="616" 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="716" 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">@@ -616,6 +716,10 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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<td class="diff-line-num old_line" data-linenumber="616" 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">
616
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<td class="diff-line-num new_line" data-linenumber="716" 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">
716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gen_quantized</span><span class="p">(</span><span class="n" style="color: #333;">quantize</span><span class="p">,</span> <span class="n" style="color: #333;">arr</span><span class="p">):</span></span>
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<td class="diff-line-num old_line" data-linenumber="617" 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">
617
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<td class="diff-line-num new_line" data-linenumber="717" 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">
717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">fquantize</span><span class="p">.</span><span class="n" style="color: #333;">write_interval</span><span class="p">(</span><span class="n" style="color: #333;">starget</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">intToStr</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="618" 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">
618
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<td class="diff-line-num new_line" data-linenumber="718" 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">
718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="nim"></span>
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<td class="diff-line-num new old_line" data-linenumber="619" 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="719" 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">
719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="nim"> <span class="n" style="color: #333;">write_summary</span><span class="p">(</span><span class="s" style="color: #d14;">"total"</span><span class="p">,</span> <span class="n" style="color: #333;">global_stat</span><span class="p">,</span> <span class="n" style="color: #333;">fh_summary</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="619" 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="720" 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">
720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">region</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="619" 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="721" 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">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="nim"> <span class="n" style="color: #333;">write_summary</span><span class="p">(</span><span class="s" style="color: #d14;">"total_region"</span><span class="p">,</span> <span class="n" style="color: #333;">global_region_stat</span><span class="p">,</span> <span class="n" style="color: #333;">fh_summary</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="619" 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="722" 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">
722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="nim"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="619" 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">
619
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<td class="diff-line-num new_line" data-linenumber="723" 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">
723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="nim"> <span class="n" style="color: #333;">write_distribution</span><span class="p">(</span><span class="s" style="color: #d14;">"total"</span><span class="p">,</span> <span class="n" style="color: #333;">global_distribution</span><span class="p">,</span> <span class="n" style="color: #333;">fh_global_dist</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="620" 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">
620
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<td class="diff-line-num new_line" data-linenumber="724" 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">
724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">region</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="621" 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">
621
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<td class="diff-line-num new_line" data-linenumber="725" 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">
725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="nim"> <span class="n" style="color: #333;">write_distribution</span><span class="p">(</span><span class="s" style="color: #d14;">"total"</span><span class="p">,</span> <span class="n" style="color: #333;">region_distribution</span><span class="p">,</span> <span class="n" style="color: #333;">fh_region_dist</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="740" 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">@@ -636,6 +740,9 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16</td>
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636
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<td class="diff-line-num new_line" data-linenumber="740" 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">
740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fthresholds</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">fthresholds</span><span class="p">)</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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637
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<td class="diff-line-num new_line" data-linenumber="741" 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">
741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span><span class="p">(</span><span class="s" style="color: #d14;">"[mosdepth] error writing thresholds file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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638
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<td class="diff-line-num new_line" data-linenumber="742" 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">
742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="nim"> <span class="n" style="color: #333;">quit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="743" 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">
743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="744" 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">
744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_d4</span><span class="p">:</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="nim"> <span class="n" style="color: #333;">fd4</span><span class="p">.</span><span class="n" style="color: #333;">close</span></span>
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639
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="nim"></span>
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640
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747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fbase</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">fbase</span><span class="p">)</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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641
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<td class="diff-line-num new_line" data-linenumber="748" 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">
748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span><span class="p">(</span><span class="s" style="color: #d14;">"[mosdepth] error writing per-base file</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="653" 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="760" 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">@@ -653,7 +760,8 @@ proc check_chrom(r: region_t, targets: seq[Target]) =</td>
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653
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">threshold_args</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">ts</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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654
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"nil"</span><span class="p">:</span></span>
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655
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span></span>
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656
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<td class="diff-line-num new_line old" data-linenumber="763" 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="LC656" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">map</span><span class="p">(</span><span class="n" style="color: #333;">ts</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">),</span> <span class="k" style="font-weight: 600;">proc</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="nim"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span><span class="p">(</span><span class="n" style="color: #333;">ts</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">),</span> <span class="k" style="font-weight: 600;">proc</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="nim"> <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">)</span></span>
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657
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="nim"></span>
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658
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="nim"></span>
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659
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">check_cram_has_ref</span><span class="p">(</span><span class="n" style="color: #333;">cram_path</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="775" 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">@@ -667,9 +775,9 @@ when(isMainModule):</td>
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667
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">release</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">lto</span><span class="p">):</span></span>
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668
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776
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span> <span class="s" style="color: #d14;">"[mosdepth] WARNING: built in debug mode; will be slow"</span></span>
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669
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="nim"></span>
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670
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"mosdepth 0.<span class="idiff left right">2.5</span>"</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"mosdepth 0.<span class="idiff left right">3.1</span>"</span></span>
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671
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">env_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getEnv</span><span class="p">(</span><span class="s" style="color: #d14;">"REF_PATH"</span><span class="p">)</span></span>
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672
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="nim"> <span class="k" style="font-weight: 600;"><span class="idiff left right">let</span></span> <span class="n" style="color: #333;">doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="nim"> <span class="k" style="font-weight: 600;"><span class="idiff left right">var</span></span> <span class="n" style="color: #333;">doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span></span>
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673
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781
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="nim"><span class="s" style="color: #d14;"> </span><span class="si" style="color: #d14;">$version</span></span>
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674
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782
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="nim"></span>
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675
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="nim"><span class="s" style="color: #d14;"> Usage: mosdepth [options] <prefix> <BAM-or-CRAM></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="677" 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="785" 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">@@ -677,6 +785,7 @@ when(isMainModule):</td>
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677
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="nim"><span class="s" style="color: #d14;">Arguments:</span></span>
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678
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="nim"></span>
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679
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="nim"><span class="s" style="color: #d14;"> <prefix> outputs: `{prefix}.mosdepth.dist.txt`</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="nim"><span class="s" style="color: #d14;"> `{prefix}.mosdepth.summary.txt`</span></span>
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680
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="nim"><span class="s" style="color: #d14;"> `{prefix}.per-base.bed.gz` (unless -n/--no-per-base is specified)</span></span>
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681
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="nim"><span class="s" style="color: #d14;"> `{prefix}.regions.bed.gz` (if --by is specified)</span></span>
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682
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="nim"><span class="s" style="color: #d14;"> `{prefix}.quantized.bed.gz` (if --quantize is specified)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="692" 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="801" 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">@@ -692,6 +801,12 @@ Common Options:</td>
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692
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="nim"><span class="s" style="color: #d14;"> -n --no-per-base dont output per-base depth. skipping this output will speed execution</span></span>
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693
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="nim"><span class="s" style="color: #d14;"> substantially. prefer quantized or thresholded values if possible.</span></span>
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694
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="nim"><span class="s" style="color: #d14;"> -f --fasta <fasta> fasta file for use with CRAM files [default: </span><span class="si" style="color: #d14;">$env_fasta</span><span class="s" style="color: #d14;">].</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="nim"><span class="s" style="color: #d14;">"""</span> <span class="o" style="font-weight: 600;">%</span> <span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">"env_fasta"</span><span class="p">,</span> <span class="n" style="color: #333;">env_fasta</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="nim"> <span class="n" style="color: #333;">doc</span> <span class="o" style="font-weight: 600;">&=</span> <span class="s" style="color: #d14;">""" --d4 output per-base depth in d4 format.</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="nim"><span class="s" style="color: #d14;">"""</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="nim"></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="nim"> <span class="n" style="color: #333;">doc</span> <span class="o" style="font-weight: 600;">&=</span> <span class="s" style="color: #d14;">"""</span></span>
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695
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="nim"></span>
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696
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="nim"><span class="s" style="color: #d14;">Other options:</span></span>
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697
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="nim"></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">@@ -699,20 +814,32 @@ Other options:</td>
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="nim"><span class="s" style="color: #d14;"> -i --include-flag <FLAG> only include reads with any of the bits in FLAG set. default is unset. [default: 0]</span></span>
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700
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="nim"><span class="s" style="color: #d14;"> -x --fast-mode dont look at internal cigar operations or correct mate overlaps (recommended for most use-cases).</span></span>
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701
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="nim"><span class="s" style="color: #d14;"> -q --quantize <segments> write quantized output see docs for description.</span></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="nim"><span class="s" style="color: #d14;"> -Q --mapq <mapq> mapping quality threshold [default: 0]</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="nim"><span class="s" style="color: #d14;"> -Q --mapq <mapq> mapping quality threshold<span class="idiff left right">. reads with a quality less than this value are ignored</span> [default: 0]</span></span>
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="nim"><span class="s" style="color: #d14;"> -T --thresholds <thresholds> for each interval in --by, write number of bases covered by at</span></span>
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704
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="nim"><span class="s" style="color: #d14;"> least threshold bases. Specify multiple integer values separated</span></span>
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705
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="nim"><span class="s" style="color: #d14;"> by ','.</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="nim"><span class="s" style="color: #d14;"> -m --use-median output median of each region (in --by) instead of mean.</span></span>
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706
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="nim"><span class="s" style="color: #d14;"> -R --read-groups <string> only calculate depth for these comma-separated read groups IDs.</span></span>
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707
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="nim"><span class="s" style="color: #d14;"> -h --help show help</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="nim"><span class="s" style="color: #d14;"> """</span> <span class="o" style="font-weight: 600;">%</span> <span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">"env_fasta"</span><span class="p">,</span> <span class="n" style="color: #333;">env_fasta</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="nim"><span class="s" style="color: #d14;"> """</span></span>
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<td class="diff-line-num new new_line" data-linenumber="825" 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">
825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="nim"></span>
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<td class="diff-line-num new old_line" data-linenumber="709" 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="826" 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">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">args</span><span class="p">:</span> <span class="n" style="color: #333;">Table</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">Value</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new old_line" data-linenumber="709" 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="827" 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">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="nim"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="709" 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="828" 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">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="nim"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">docopt</span><span class="p">(</span><span class="n" style="color: #333;">doc</span><span class="p">,</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="n" style="color: #333;">quit</span><span class="o" style="font-weight: 600;">=</span><span class="kp" style="font-weight: 600;">false</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="709" 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="829" 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">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="nim"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">DocoptExit</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="709" 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="830" 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">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="p">(</span><span class="k" style="font-weight: 600;">ref</span> <span class="n" style="color: #333;">DocoptExit</span><span class="p">)(</span><span class="n" style="color: #333;">get_current_exception</span><span class="p">()).</span><span class="n" style="color: #333;">usage</span></span>
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<td class="diff-line-num new old_line" data-linenumber="709" 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="831" 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">
831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="nim"> <span class="n" style="color: #333;">quit</span> <span class="s" style="color: #d14;">"error parsing arguments"</span></span>
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<td class="diff-line-num old_line" data-linenumber="709" 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">
709
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<td class="diff-line-num new_line" data-linenumber="832" 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">
832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="710" 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">
710
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<td class="diff-line-num new_line old" data-linenumber="833" 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="LC710" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">docopt</span><span class="p">(</span><span class="n" style="color: #333;">doc</span><span class="p">,</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="711" 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">
711
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<td class="diff-line-num new_line" data-linenumber="833" 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">
833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="nim"> <span class="k" style="font-weight: 600;">let</span> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">S</span><span class="p">.</span><span class="n" style="color: #333;">parse_int</span><span class="p">(</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--mapq"</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="712" 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">
712
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<td class="diff-line-num new_line" data-linenumber="834" 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">
834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span></span>
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<td class="diff-line-num old_line" data-linenumber="713" 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">
713
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<td class="diff-line-num new_line" data-linenumber="835" 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">
835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="nim"> <span class="n" style="color: #333;">region</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">string</span></span>
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<td class="diff-line-num old_line" data-linenumber="714" 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">
714
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<td class="diff-line-num new_line" data-linenumber="836" 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">
836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="nim"> <span class="n" style="color: #333;">thresholds</span><span class="p">:</span> <span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threshold_args</span><span class="p">(</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--thresholds"</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="715" 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">
715
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<td class="diff-line-num new_line" data-linenumber="837" 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">
837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="nim"> <span class="n" style="color: #333;">fast_mode</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--fast-mode"</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new old_line" data-linenumber="716" 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="838" 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">
838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="nim"> <span class="n" style="color: #333;">use_median</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--use-median"</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new old_line" data-linenumber="716" 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="839" 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">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="nim"> <span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">d4</span><span class="p">):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="716" 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="840" 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">
840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">use_d4</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--d4"</span><span class="o" style="font-weight: 600;">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--no-per-base"</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="841" 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">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="842" 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">
842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">use_d4</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">false</span></span>
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716
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="nim"></span>
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717
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--by"</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"nil"</span><span class="p">:</span></span>
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718
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="nim"> <span class="n" style="color: #333;">region</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="s" style="color: #d14;">"--by"</span><span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" 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="875" 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">@@ -748,4 +875,4 @@ Other options:</td>
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748
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="n" style="color: #333;">FormatOption</span><span class="p">.</span><span class="n" style="color: #333;">CRAM_OPT_DECODE_MD</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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749
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<td class="diff-line-num new_line" data-linenumber="876" 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">
876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="nim"> <span class="n" style="color: #333;">check_chrom</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">bam</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">.</span><span class="n" style="color: #333;">targets</span><span class="p">)</span></span>
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750
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="nim"></span>
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751
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="nim"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">mapq</span><span class="p">,</span> <span class="n" style="color: #333;">eflag</span><span class="p">,</span> <span class="n" style="color: #333;">iflag</span><span class="p">,</span> <span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">thresholds</span><span class="p">,</span> <span class="n" style="color: #333;">fast_mode</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">)</span></span></pre>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="nim"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">mapq</span><span class="p">,</span> <span class="n" style="color: #333;">eflag</span><span class="p">,</span> <span class="n" style="color: #333;">iflag</span><span class="p">,</span> <span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="n" style="color: #333;">thresholds</span><span class="p">,</span> <span class="n" style="color: #333;">fast_mode</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_median</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">use_median</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_d4</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">use_d4</span></span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#a99b7e9ffb6c06b4832f1c7ce8d8dbbf023f7502"><strong>mosdepth.nimble</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Package</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">version = "0.<span class="idiff left right">2.5</span>"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">version = "0.<span class="idiff left right">3.1</span>"</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">author = "Brent Pedersen"</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">description = "fast depth"</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">license = "MIT"</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># Dependencies</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">requires "hts >= 0.<span class="idiff left right">2.7", "docopt >= 0.6.8</span>"</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">requires "hts >= 0.<span class="idiff left right">3.1", "docopt >= 0.6.8", "nim >= 1.0.0", "https://github.com/brentp/d4-nim</span>"</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">bin = @["mosdepth"]</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">skipDirs = @["tests"]</span>
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<li id="1f022802374dbfb04433943a561ed4b5f0e0aa25">
<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#1f022802374dbfb04433943a561ed4b5f0e0aa25"><strong>scripts/install.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">@@ -21,10 +21,26 @@ cd $base</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell">nimble refresh</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">$base</span>/nim-<span class="nv" style="color: #008080;">$BRANCH</span>/bin/nimble <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">git clone <span class="nt" style="color: #000080;">--recursive</span> https://github.com/samtools/htslib.git</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">curl <span class="nt" style="color: #000080;">--proto</span> <span class="s1" style="color: #d14;">'=https'</span> <span class="nt" style="color: #000080;">--tlsv1</span>.2 <span class="nt" style="color: #000080;">-sSf</span> https://sh.rustup.rs | sh <span class="nt" style="color: #000080;">-s</span> <span class="nt" style="color: #000080;">--</span> <span class="nt" style="color: #000080;">-qy</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HTSLIB</span><span class="o" style="font-weight: 600;">=</span>dynamic</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sudo </span>apt-get update</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sudo </span>apt-get <span class="nb" style="color: #0086b3;">install </span>git llvm curl wget libcurl4-openssl-dev</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">wget https://github.com/samtools/htslib/archive/1.10.2.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>xzf 1.10.2.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>htslib-1.10.2/</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">autoheader <span class="o" style="font-weight: 600;">&&</span> autoconf <span class="o" style="font-weight: 600;">&&</span> ./configure <span class="nt" style="color: #000080;">--enable-libcurl</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sudo </span>make <span class="nt" style="color: #000080;">-j4</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">git clone https://github.com/38/d4-format</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>d4-format</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">~/.cargo/bin/cargo build <span class="nt" style="color: #000080;">--release</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sudo cp</span> ../d4-format/target/release/libd4binding.<span class="k" style="font-weight: 600;">*</span> /usr/local/lib</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sudo cp</span> ./d4binding/include/d4.h /usr/local/include/</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sudo </span>ldconfig</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>htslib <span class="o" style="font-weight: 600;">&&</span> git checkout 1.9 <span class="o" style="font-weight: 600;">&&</span> autoheader <span class="o" style="font-weight: 600;">&&</span> autoconf <span class="o" style="font-weight: 600;">&&</span> ./configure <span class="nt" style="color: #000080;">--enable-libcurl</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell">make <span class="nt" style="color: #000080;">-j</span> 4 <span class="nt" style="color: #000080;">-C</span> htslib</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LD_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$base</span>/htslib</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-lh</span> <span class="nv" style="color: #008080;">$base</span>/htslib/<span class="k" style="font-weight: 600;">*</span>.so</span></pre>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LD_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$base</span>/htslib-1.10.2</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-lh</span> <span class="nv" style="color: #008080;">$base</span>/htslib-1.10.2/<span class="k" style="font-weight: 600;">*</span>.so</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell">nimble <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> https://github.com/brentp/d4-nim/</span></pre>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#ec55c77e5315f22521ed1a772a398adb082f28e3"><strong>scripts/plot-dist.py</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">@@ -19,6 +19,9 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">data</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">it</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="n" style="color: #333;">gen</span><span class="p">,</span> <span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)):</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"GL"</span><span class="p">):</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Un"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"random"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"HLA"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chrom</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"alt"</span><span class="p">):</span> <span class="k" style="font-weight: 600;">continue</span></span>
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22
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">chroms</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">xs</span><span class="p">,</span> <span class="n" style="color: #333;">ys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">v50</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<a href="https://salsa.debian.org/med-team/mosdepth/-/commit/4466b30323ddf13b4a4806f7dffdf33d0d7001de#5c05cfa4f939f387afdf0c5360196139984517fd"><strong>tests/funcs.nim</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">unittest</span><span class="p">,</span> <span class="n" style="color: #333;">mosdepth</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mosdepth</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">unittest</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">mosdepth</span></span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="nim"></span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="nim"><span class="n" style="color: #333;">suite</span> <span class="s" style="color: #d14;">"mosdepth-suite"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="64" 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="65" 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">@@ -64,6 +65,14 @@ suite "mosdepth-suite":</td>
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64
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<td class="diff-line-num new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">ts</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>
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65
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<td class="diff-line-num new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">ts</span><span class="p">.</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>
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66
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="nim"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="nim"> <span class="n" style="color: #333;">test</span> <span class="s" style="color: #d14;">"name splitting"</span><span class="p">:</span></span>
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67
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region_line_to_region</span><span class="p">(</span><span class="s" style="color: #d14;">"Super-Scaffold_52"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Super-Scaffold_52"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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68
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="nim"></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="nim"></span></pre>
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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="nim"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region_line_to_region</span><span class="p">(</span><span class="s" style="color: #d14;">"Super-Scaffold_52:2-1000"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Super-Scaffold_52"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="70" 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="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="nim"> <span class="n" style="color: #333;">check</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1000</span></span></pre>
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