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GitLab

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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/delly">Debian Med / delly</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089">77fba0a1</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2020-10-02T14:30:54+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.5</pre>

</li>

</ul>

<h4>26 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8b09b55769c028063c592c342ad7e6b2689e6547">

<span class="new-file">

+

.github/workflows/c-cpp.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#6a7d105cee155e00142e5ced05fbd9aa83f45b8b">

<span class="new-file">

+

.github/workflows/docker.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">

docker/Dockerfile

→

Dockerfile

</a>

</li>

<li class="file-stats">

<a href="#a17bb5ab7d570c1052a54b68459323d663d401b9">

<span class="new-file">

+

R/gcbias.R

</span>

</a>

</li>

<li class="file-stats">

<a href="#5f978958190b293037054bd9d5e795d0b92d1ca8">

<span class="new-file">

+

R/rd.R

</span>

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#24b66ee316591fa3a67bfac872969a7ad776ac9e">

<span class="deleted-file">

−

docker/README.md

</span>

</a>

</li>

<li class="file-stats">

<a href="#ee39e20c808b311e42961e3a772756178a5b5049">

singularity/delly.def

</a>

</li>

<li class="file-stats">

<a href="#09127824dfd1dcb511663f94ed3fb9ad5e9d7d5e">

<span class="new-file">

+

src/bed.h

</span>

</a>

</li>

<li class="file-stats">

<a href="#d0a709faa909252ae246c0d6c1212099d4cc6343">

src/cluster.h

</a>

</li>

<li class="file-stats">

<a href="#6a965fc172da372b399f988708853bec938e4290">

<span class="new-file">

+

src/cnv.h

</span>

</a>

</li>

<li class="file-stats">

<a href="#dcad3ddfd75218047069bbaa2acab307a0655169">

<span class="new-file">

+

src/coral.h

</span>

</a>

</li>

<li class="file-stats">

<a href="#e19d274a46472d34d39a42180498e5c30d7e7424">

src/coverage.h

</a>

</li>

<li class="file-stats">

<a href="#5d775c4d26336d72c9aaeefa6f42a658ef123ac9">

src/delly.cpp

</a>

</li>

<li class="file-stats">

<a href="#959a235a0b48a27af0667cc50c53360de917157d">

src/delly.h

</a>

</li>

<li class="file-stats">

<a href="#bd5bcc3550f5a1f8c55a54de46b962722805f66a">

<span class="new-file">

+

src/gcbias.h

</span>

</a>

</li>

<li class="file-stats">

<a href="#836bf99511b7d355c156c4bd68f24fd0b7ce69c9">

src/genotype.h

</a>

</li>

<li class="file-stats">

<a href="#88ce703739571701e1144b45c8b9e7a2ef9dd1c1">

src/merge.h

</a>

</li>

<li class="file-stats">

<a href="#961fb7e93e491fbba61e895bde9438ca23a92e42">

src/modvcf.h

</a>

</li>

<li class="file-stats">

<a href="#3c321c0c9f85ac1d870308c56630d8d53e324018">

src/needle.h

</a>

</li>

<li class="file-stats">

<a href="#5165b8164503f1ee0f58727e13103d7a1f7b025b">

<span class="new-file">

+

src/scan.h

</span>

</a>

</li>

<li class="file-stats">

<a href="#76bf896cda9e6b76c0af8350e53bb4bc92d6d281">

src/tags.h

</a>

</li>

<li class="file-stats">

<a href="#0295016a39c777dffa48c5e5efc6af0fb6982a0a">

src/tegua.h

</a>

</li>

<li class="file-stats">

<a href="#5f65ec0c183df81ed169516d4ec6c5508122dccd">

src/util.h

</a>

</li>

<li class="file-stats">

<a href="#f92b0b9f2ecd99eca4c19d9518afaae33bc2d58a">

src/version.h

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="8b09b55769c028063c592c342ad7e6b2689e6547">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#8b09b55769c028063c592c342ad7e6b2689e6547"><strong>.github/workflows/c-cpp.yml</strong></a>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">C/C++ CI</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">  <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml">    <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">master</span> <span class="pi">]</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">  <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>

</pre>

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7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml">    <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">master</span> <span class="pi">]</span></span>

</pre>

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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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"></span>

</pre>

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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">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml">  <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"></span>

</pre>

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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="yaml">    <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>

</pre>

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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="yaml">    <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" 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>

</pre>

</td>

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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="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">make</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml">      <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml">        <span class="s" style="color: #d14;">sudo apt-get update</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml">        <span class="s" style="color: #d14;">sudo apt-get install -y libcurl4-gnutls-dev libhts-dev libhts2 libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml">        <span class="s" style="color: #d14;">make</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="6a7d105cee155e00142e5ced05fbd9aa83f45b8b">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#6a7d105cee155e00142e5ced05fbd9aa83f45b8b"><strong>.github/workflows/docker.yml</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Docker CI</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">  <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml">    <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">master</span> <span class="pi">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">  <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml">    <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">master</span> <span class="pi">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml">  <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml">    <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml">    <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" 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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker/build-push-action@v1</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml">      <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml">        <span class="na" style="color: #008080;">username</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.DOCKER_USERNAME }}</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml">        <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.DOCKER_PASSWORD }}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml">        <span class="na" style="color: #008080;">repository</span><span class="pi">:</span> <span class="s" style="color: #d14;">dellytools/delly</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml">        <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="s" style="color: #d14;">latest</span></span></pre>

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<br>

</li>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#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">@@ -54,9 +54,6 @@ matrix:</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="yaml">          <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">g++-9</span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">MYCC="gcc" MYCXX="g++"</span></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml">      <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="yaml">      <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode8.3</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">MYCC="gcc" MYCXX="g++"</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="yaml">      <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="yaml">      <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode11.3</span></span>

</pre>

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<br>

</li>

<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>docker/Dockerfile</strong>

→

<strong>Dockerfile</strong>

</a>

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<li id="a17bb5ab7d570c1052a54b68459323d663d401b9">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#a17bb5ab7d570c1052a54b68459323d663d401b9"><strong>R/gcbias.R</strong></a>

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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="r"><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">ggplot2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="r"><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">reshape2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="r"></span>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="r"><span class="n" style="color: #333;">args</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">commandArgs</span><span class="p">(</span><span class="n" style="color: #333;">trailingOnly</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">TRUE</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">read.table</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="p">],</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">T</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">read.table</span><span class="p">(</span><span class="s2" style="color: #d14;">"gc.table"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">T</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">gc</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">gcsum</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">/</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span><span class="m" style="color: #099;">-1</span><span class="p">)</span></span>

</pre>

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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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fractionSample</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fractionSample</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">*</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">100</span></span>

</pre>

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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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fractionReference</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fractionReference</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">*</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">100</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="r"><span class="n" style="color: #333;">df</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">melt</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"gc"</span><span class="p">,</span><span class="s2" style="color: #d14;">"fractionSample"</span><span class="p">,</span><span class="s2" style="color: #d14;">"fractionReference"</span><span class="p">)],</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">id.vars</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"gc"</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="r"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># Whole genome</span></span>

</pre>

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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="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ggplot</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">df</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gc</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">value</span><span class="p">))</span></span>

</pre>

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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="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">geom_bar</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">variable</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">fill</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">variable</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">stat</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"identity"</span><span class="p">)</span></span>

</pre>

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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="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xlab</span><span class="p">(</span><span class="s2" style="color: #d14;">"GC content"</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylab</span><span class="p">(</span><span class="s2" style="color: #d14;">"Obs / Exp"</span><span class="p">)</span></span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylim</span><span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">obsexp</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fractionSample</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fractionReference</span><span class="p">)))</span></span>

</pre>

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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="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">geom_line</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gc</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">obsexp</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"black"</span><span class="p">)</span></span>

</pre>

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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="r"><span class="n" style="color: #333;">ggsave</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"gcbias.png"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">12</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">height</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">6</span><span class="p">)</span></span>

</pre>

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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="r"><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">warnings</span><span class="p">())</span></span></pre>

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</table>

<br>

</li>

<li id="5f978958190b293037054bd9d5e795d0b92d1ca8">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#5f978958190b293037054bd9d5e795d0b92d1ca8"><strong>R/rd.R</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="r"><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">ggplot2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="r"><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">scales</span><span class="p">)</span></span>

</pre>

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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="r"><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">gtable</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="r"><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">grid</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="r"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="r"><span class="n" style="color: #333;">chrNamesLong</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"chr1"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr2"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr3"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr4"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr5"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr6"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr7"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr8"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr9"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr10"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr11"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr12"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr13"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr14"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr15"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr16"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr17"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr18"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr19"</span><span class="p">,</span><span class="s2" style="color: #d14;">"chr20"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"chr21"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"chr22"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"chrX"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="r"><span class="n" style="color: #333;">chrNamesShort</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"1"</span><span class="p">,</span><span class="s2" style="color: #d14;">"2"</span><span class="p">,</span><span class="s2" style="color: #d14;">"3"</span><span class="p">,</span><span class="s2" style="color: #d14;">"4"</span><span class="p">,</span><span class="s2" style="color: #d14;">"5"</span><span class="p">,</span><span class="s2" style="color: #d14;">"6"</span><span class="p">,</span><span class="s2" style="color: #d14;">"7"</span><span class="p">,</span><span class="s2" style="color: #d14;">"8"</span><span class="p">,</span><span class="s2" style="color: #d14;">"9"</span><span class="p">,</span><span class="s2" style="color: #d14;">"10"</span><span class="p">,</span><span class="s2" style="color: #d14;">"11"</span><span class="p">,</span><span class="s2" style="color: #d14;">"12"</span><span class="p">,</span><span class="s2" style="color: #d14;">"13"</span><span class="p">,</span><span class="s2" style="color: #d14;">"14"</span><span class="p">,</span><span class="s2" style="color: #d14;">"15"</span><span class="p">,</span><span class="s2" style="color: #d14;">"16"</span><span class="p">,</span><span class="s2" style="color: #d14;">"17"</span><span class="p">,</span><span class="s2" style="color: #d14;">"18"</span><span class="p">,</span><span class="s2" style="color: #d14;">"19"</span><span class="p">,</span><span class="s2" style="color: #d14;">"20"</span><span class="p">,</span><span class="s2" style="color: #d14;">"21"</span><span class="p">,</span><span class="s2" style="color: #d14;">"22"</span><span class="p">,</span><span class="s2" style="color: #d14;">"X"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="r"></span>

</pre>

</td>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="r"><span class="n" style="color: #333;">args</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">commandArgs</span><span class="p">(</span><span class="n" style="color: #333;">trailingOnly</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">TRUE</span><span class="p">)</span></span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">read.table</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="p">],</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">T</span><span class="p">)</span></span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="r"><span class="n" style="color: #333;">maxCN</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">8</span></span>

</pre>

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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="r"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># Fix chromosome ordering</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="r"><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%in%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrNamesLong</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">></span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%in%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrNamesShort</span><span class="p">))</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrNamesLong</span><span class="p">;</span><span class="w" style="color: #bbb;"> </span><span class="p">}</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrNamesShort</span><span class="p">;</span><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%in%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrs</span><span class="p">,]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">factor</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">levels</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chrs</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="r"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># Whole genome</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ggplot</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">[,</span><span class="m" style="color: #099;">6</span><span class="p">]))</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">geom_point</span><span class="p">(</span><span class="n" style="color: #333;">pch</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">21</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">0.5</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xlab</span><span class="p">(</span><span class="s2" style="color: #d14;">"Chromosome"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylab</span><span class="p">(</span><span class="s2" style="color: #d14;">"Copy-number"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">scale_x_continuous</span><span class="p">(</span><span class="n" style="color: #333;">labels</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">comma</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">facet_grid</span><span class="p">(</span><span class="n" style="color: #333;">.</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">~</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chr</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">scales</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"free_x"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">space</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"free_x"</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylim</span><span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">maxCN</span><span class="p">)</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="r"><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">theme</span><span class="p">(</span><span class="n" style="color: #333;">axis.text.x</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">element_text</span><span class="p">(</span><span class="n" style="color: #333;">angle</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">45</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">hjust</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="r"><span class="n" style="color: #333;">ggsave</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"plot.wholegenome.png"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">24</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">height</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">6</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="r"><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">warnings</span><span class="p">())</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="r"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># By chromosome</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="r"><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">chrname</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">in</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">unique</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="p">))</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">chrname</span><span class="p">)</span></span>

</pre>

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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="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sub</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">==</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrname</span><span class="p">,]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ggplot</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sub</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sub</span><span class="p">[,</span><span class="m" style="color: #099;">6</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">geom_point</span><span class="p">(</span><span class="n" style="color: #333;">pch</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">21</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">0.5</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylab</span><span class="p">(</span><span class="s2" style="color: #d14;">"Copy-number"</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xlab</span><span class="p">(</span><span class="n" style="color: #333;">chrname</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">scale_x_continuous</span><span class="p">(</span><span class="n" style="color: #333;">labels</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">comma</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">breaks</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">scales</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pretty_breaks</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">20</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylim</span><span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">maxCN</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="39" 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="LC39" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">+</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">theme</span><span class="p">(</span><span class="n" style="color: #333;">axis.text.x</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">element_text</span><span class="p">(</span><span class="n" style="color: #333;">angle</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">45</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">hjust</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ggsave</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">paste0</span><span class="p">(</span><span class="s2" style="color: #d14;">"plot."</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrname</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">".png"</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">24</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">height</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">6</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">warnings</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="r"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="r"></span></pre>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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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">@@ -7,11 +7,10 @@</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![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/delly/README.html)</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Anaconda-Server Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/delly/badges/downloads.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/delly)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" 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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<td class="diff-line-num new_line old" data-linenumber="10" 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="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![<span class="idiff left">Build Status</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://travis-ci.org/dellytools/delly.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.org/dellytools/delly</span>)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker <span class="idiff left">Build</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">https://img.shields.io/docker/build/dellytools/delly</span>.svg</span><span class="p">)</span>](https://hub.docker.com/r/dellytools/delly/)</span>

</pre>

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<td class="diff-line-num new old_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">

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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;">![<span class="idiff left">C/C++ CI</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/dellytools/delly/workflows/C/C++%20CI/badge.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://github.com/dellytools/delly/actions</span>)</span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker <span class="idiff left">CI</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">https://github.com/dellytools/delly/workflows/Docker%20CI/badge</span>.svg</span><span class="p">)</span>](https://hub.docker.com/r/dellytools/delly/)</span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![GitHub license</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-BSD%203--Clause-blue.svg</span><span class="p">)</span>](https://github.com/dellytools/delly/blob/master/LICENSE)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![GitHub Releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/release/dellytools/delly.svg</span><span class="p">)</span>](https://github.com/dellytools/delly/releases)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" 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="LC14" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![GitHub Issues</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/issues/dellytools/delly.svg</span><span class="p">)</span>](https://github.com/dellytools/delly/issues)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown">Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using <span class="p">[</span><span class="nv" style="color: #008080;">Delly-maze</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/dellytools/maze</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">Delly-suave</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/dellytools/suave</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="36" 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">@@ -37,9 +36,6 @@ Delly supports parallel computing using the OpenMP API (www.openmp.org).</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="sb" style="color: #d14;">`make PARALLEL=1 -B src/delly`</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="39" 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="LC40" class="line" lang="markdown">There is also a statically linked, multi-threaded binary for Linux 64-bit available under <span class="p">[</span><span class="nv" style="color: #008080;">releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/dellytools/delly/releases/</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="39" 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="LC41" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" 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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<td class="diff-line-num new_line old" data-linenumber="39" 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="LC42" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown">You can set the number of threads using the environment variable OMP_NUM_THREADS.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="sb" style="color: #d14;">`export OMP_NUM_THREADS=2`</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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="54" 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">@@ -58,6 +54,16 @@ Delly needs a sorted, indexed and duplicate marked bam file for every input samp</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bcftools view delly.bcf > delly.vcf`</span></span>

</pre>

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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"></span>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="57" 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="LC57" class="line" lang="markdown"><span class="gh" style="color: #999;">Delly for long reads from PacBio or ONT (experimental)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------------------------------------</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="60" 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="LC60" class="line" lang="markdown">Delly also has a long-read SV discovery mode.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="62" 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="LC62" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly lr -y ont -g hg19.fa -x hg19.excl input.bam`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"></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">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly lr -y pb -g hg19.fa -x hg19.excl input.bam`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"><span class="gh" style="color: #999;">Somatic SV calling</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="110" 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">@@ -104,34 +110,53 @@ Germline SV calling</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly filter -f germline -o germline.bcf merged.bcf`</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="114" 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="LC114" class="line" lang="markdown"><span class="gh" style="color: #999;">Read-depth profiles</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="115" 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="LC115" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="116" 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="LC116" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="markdown">You can generate read-depth profiles with delly. This requires a mappability map which can be downloaded here:</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="118" 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="LC118" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Mappability Maps</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gear.embl.de/data/delly/</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="120" 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="LC120" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="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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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown">The command to count reads in 10kbp windows and normalize the coverage is:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="122" 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">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="123" 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="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly rd -a -g hg19.fa -m hg19.map input.bam`</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="124" 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="LC124" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="125" 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="LC125" class="line" lang="markdown">The output file can be plotted using R to generate normalized copy-number profiles:</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="126" 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="LC126" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="127" 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="LC127" class="line" lang="markdown"><span class="sb" style="color: #d14;">`Rscript R/rd.R out.cov.gz`</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="128" 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="LC128" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="129" 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="LC129" class="line" lang="markdown">The GC bias can be visualized using the stats output.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="130" 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="LC130" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="131" 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="LC131" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly rd -s stats.gz -g hg19.fa -m hg19.map input.bam`</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="132" 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="LC132" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="133" 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="LC133" class="line" lang="markdown"><span class="sb" style="color: #d14;">`zgrep "^GC" stats.gz  > gc.table`</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="134" 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="LC134" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="135" 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="LC135" class="line" lang="markdown"><span class="sb" style="color: #d14;">`Rscript R/gcbias.R gc.table`</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="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">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="137" 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="LC137" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="gh" style="color: #999;">FAQ</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="139" 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">

139

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"><span class="gh" style="color: #999;">---</span></span>

</pre>

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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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<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="markdown"><span class="p">*</span> What is the smallest SV size Delly can call?  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" 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">

110

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<td class="diff-line-num new_line old" data-linenumber="141" 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="LC110" class="line" lang="markdown">This depends on the sharpness of the insert size distribution. For an insert size of 200-300bp with a 20-30bp standard deviation, Delly starts to call reliable SVs >=300bp. Delly also supports calling of small InDels using soft-clipped reads only (-i option). In this mode the smallest SV size called is 15bp.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" 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">

111

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<td class="diff-line-num new_line old" data-linenumber="141" 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="LC111" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" 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">

112

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<td class="diff-line-num new_line old" data-linenumber="141" 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="LC112" class="line" lang="markdown"><span class="p">*</span> Is Delly read-group aware?   </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" 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">

113

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<td class="diff-line-num new_line old" data-linenumber="141" 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="LC113" class="line" lang="markdown">Yes. If you want to estimate separate insert size distributions for every read-group then use the -e option.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="141" 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="LC141" class="line" lang="markdown">This depends on the sharpness of the insert size distribution. For an insert size of 200-300bp with a 20-30bp standard deviation, Delly starts to call reliable SVs >=300bp. Delly also supports calling of small InDels using soft-clipped reads only, the smallest SV size called is 15bp.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" 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">

114

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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="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" 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">

115

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"><span class="p">*</span> Can Delly be used on a non-diploid genome?  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" 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">

116

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown">Yes and no. The SV site discovery works for any ploidy. However, Delly's genotyping model assumes diploidy (hom. reference, het. and hom. alternative).</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="117" 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">

117

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<td class="diff-line-num new_line" data-linenumber="145" 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">

145

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"></span>

</pre>

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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">

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<td class="diff-line-num new_line old" data-linenumber="146" 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="LC118" class="line" lang="markdown"><span class="p">*</span> How do I run Delly if I have multiple different libraries/bam files for a single sample?    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" 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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<td class="diff-line-num new_line old" data-linenumber="146" 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="LC119" class="line" lang="markdown">Merge these BAMs using tools such as <span class="p">[</span><span class="nv" style="color: #008080;">Picard</span><span class="p">](</span><span class="sx" style="color: #d14;">http://broadinstitute.github.io/picard/</span><span class="p">)</span> and tag each library with a unique ReadGroup. If you have a sample with multiple read-groups please run delly with the -e option.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" 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">

120

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<td class="diff-line-num new_line old" data-linenumber="146" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC120" class="line" lang="markdown"></span>

</pre>

</td>

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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="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"><span class="p">*</span> Delly is running too slowly what can I do?    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" 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">

122

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<td class="diff-line-num new_line old" data-linenumber="147" 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="LC122" class="line" lang="markdown">You should exclude telomere and centromere regions and also all unplaced contigs. Delly ships with such an exclude list for human and mouse samples. In addition, you can filter input reads more stringently using -q 20 and -s 15.<span class="idiff left right"> Small InDel calling takes more time (-i option), leave it out if you are only interested in large SVs (>=300bp).</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="123" 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="147" 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="LC147" class="line" lang="markdown">You should exclude telomere and centromere regions and also all unplaced contigs. Delly ships with such an exclude list for human and mouse samples. In addition, you can filter input reads more stringently using -q 20 and -s 15.</span>

</pre>

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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="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown"><span class="p">*</span> Are non-unique alignments, multi-mappings and/or multiple split-read alignments allowed?  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" 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">

125

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<td class="diff-line-num new_line old" data-linenumber="150" 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="LC125" class="line" lang="markdown">Delly expects two alignment records in the bam file for every paired-end, one for the first and one for the second read. Multiple split-read alignment records of a given read are allowed if and only if one of them <span class="idiff left right">(e.g. the longest split alignment) </span>is a primary alignment whereas all others are marked as secondary or supplementary (flag 0x0100 or flag 0x0800). This is the default for bwa mem.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" 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="150" 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="LC150" class="line" lang="markdown">Delly expects two alignment records in the bam file for every paired-end, one for the first and one for the second read. Multiple split-read alignment records of a given read are allowed if and only if one of them is a primary alignment whereas all others are marked as secondary or supplementary (flag 0x0100 or flag 0x0800). This is the default for bwa mem.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" 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">

126

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<td class="diff-line-num new_line" data-linenumber="151" 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">

151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" 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">

127

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<td class="diff-line-num new_line" data-linenumber="152" 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">

152

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown"><span class="p">*</span> What pre-processing of bam files is required?    </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="128" 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">

128

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<td class="diff-line-num new_line old" data-linenumber="153" 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="LC128" class="line" lang="markdown">Bam files need to be sorted, indexed and ideally duplicate marked.<span class="idiff left right"> If multiple libraries are present for a single sample these need to be merged in a single bam file with unique ReadGroup tags.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="129" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="markdown">Bam files need to be sorted, indexed and ideally duplicate marked.</span>

</pre>

</td>

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<td class="diff-line-num 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">

129

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<td class="diff-line-num new_line" data-linenumber="154" 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">

154

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC154" class="line" lang="markdown"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="130" 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">

130

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<td class="diff-line-num new_line" data-linenumber="155" 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">

155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"><span class="p">*</span> Usage/discussion mailing list?         </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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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<td class="diff-line-num 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">

156

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown">There is a delly discussion group <span class="p">[</span><span class="nv" style="color: #008080;">delly-users</span><span class="p">](</span><span class="sx" style="color: #d14;">http://groups.google.com/d/forum/delly-users</span><span class="p">)</span>.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="132" 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">

132

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<td class="diff-line-num new_line" data-linenumber="157" 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">

157

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="133" 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">

133

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<td class="diff-line-num new_line old" data-linenumber="158" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC133" class="line" lang="markdown"><span class="p">*</span> Docker support?            </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="134" 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">

134

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<td class="diff-line-num new_line old" data-linenumber="158" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC134" class="line" lang="markdown">There is a dockerized delly available <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/dellytools/delly/</span><span class="p">)</span>.</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="135" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="158" 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="LC158" class="line" lang="markdown"><span class="p">*</span> Docker<span class="idiff left right">/Singularity</span> support?            </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="135" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="159" 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="LC159" class="line" lang="markdown">There is a dockerized delly available <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/dellytools/delly/</span><span class="p">)</span><span class="idiff left"> and singularity containers (</span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">*</span></span><span class="idiff">.sif files) are part of the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">delly release</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/dellytools/delly/releases</span></span><span class="p"><span class="idiff right">)</span></span>.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="135" 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">

135

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<td class="diff-line-num new_line" data-linenumber="160" 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">

160

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="136" 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">

136

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<td class="diff-line-num new_line" data-linenumber="161" 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">

161

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="markdown"><span class="p">*</span> Bioconda support?             </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown">Delly is available via <span class="p">[</span><span class="nv" style="color: #008080;">bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bioconda.github.io/recipes/delly/README.html</span><span class="p">)</span>.</span>

</pre>

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<br>

</li>

<li id="24b66ee316591fa3a67bfac872969a7ad776ac9e">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#24b66ee316591fa3a67bfac872969a7ad776ac9e"><strong>docker/README.md</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Dockerized Delly</span></span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" 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="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Delly</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/dellytools/delly</span><span class="p">)</span> is available as a <span class="p">[</span><span class="nv" style="color: #008080;">Docker image</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/dellytools/delly/</span><span class="p">)</span>. You can pull the Delly image using</span>

</pre>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="sb" style="color: #d14;">`docker pull dellytools/delly`</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">You can then run Delly from that image. Below we assume your alignment files in BAM format are in /var/data which is mounted as /root in the docker container.</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="sb" style="color: #d14;">`docker run -it -v /var/data/:/root dellytools/delly`</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">The container by default starts a shell which you can then use to run Delly.</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly call -o /root/sv.bcf -g /root/ref.fa /root/control.bam /root/tumor.bam`</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">Once Delly is finished you can just exit the Docker image.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="sb" style="color: #d14;">`exit`</span></span></pre>

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<br>

</li>

<li id="ee39e20c808b311e42961e3a772756178a5b5049">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#ee39e20c808b311e42961e3a772756178a5b5049"><strong>singularity/delly.def</strong></a>

<hr>

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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">@@ -17,7 +17,7 @@ Stage: build</td>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># Final image</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">BootStrap: library</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC20" class="line" lang="plaintext">From: alpine:<span class="idiff left right">3.9</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">From: alpine:<span class="idiff left right">latest</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Stage: final</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" 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">

22

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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">

23

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<td class="diff-line-num new_line" data-linenumber="23" 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">

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">%files from build</span>

</pre>

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<br>

</li>

<li id="09127824dfd1dcb511663f94ed3fb9ad5e9d7d5e">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#09127824dfd1dcb511663f94ed3fb9ad5e9d7d5e"><strong>src/bed.h</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef BED_H</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define BED_H</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="4" 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="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/filesystem.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="5" 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="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/multi_array.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="6" 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="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/progress.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/posix_time/posix_time.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/unordered_map.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/algorithm/string.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="10" 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="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/tokenizer.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/math/distributions/chi_squared.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/math/distributions/hypergeometric.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filtering_streambuf.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filtering_stream.hpp></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/copy.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filter/gzip.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/device/file.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filter/zlib.hpp></span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/faidx.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/vcf.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/sam.h></span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">torali</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Flattens overlapping intervals</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TRegionsGenome</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">    <span class="n" style="color: #333;">_parseBedIntervals</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">filePresent</span><span class="p">,</span> <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">TRegionsGenome</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TRegionsGenome</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">interval_type</span> <span class="n" style="color: #333;">TIVal</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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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="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filePresent</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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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="cpp">      <span class="n" style="color: #333;">bedRegions</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">,</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="p">());</span></span>

</pre>

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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="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">chrFile</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrFile</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">chrFile</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">chrFromFile</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp">     <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">chrFile</span><span class="p">,</span> <span class="n" style="color: #333;">chrFromFile</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tokenizer</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">char_separator</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Tokenizer</span><span class="p">;</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">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">     <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">char_separator</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sep</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>

</pre>

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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="cpp">     <span class="n" style="color: #333;">Tokenizer</span> <span class="n" style="color: #333;">tokens</span><span class="p">(</span><span class="n" style="color: #333;">chrFromFile</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">     <span class="n" style="color: #333;">Tokenizer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">tokIter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokIter</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" 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="LC47" class="line" lang="cpp">       <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">chrName</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tokIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">       <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_name2id</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">chrName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="49" 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="LC49" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tid</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>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokIter</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">           <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lexical_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</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;">tokIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">           <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lexical_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</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;">tokIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp">           <span class="n" style="color: #333;">bedRegions</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">TIVal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">right_open</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp">           <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">intervals</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp">       <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">     <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">      <span class="n" style="color: #333;">chrFile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">intervals</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Keeps overlapping intervals</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TRegionsGenome</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">  <span class="n" style="color: #333;">_parsePotOverlappingIntervals</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">filePresent</span><span class="p">,</span> <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">TRegionsGenome</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TRegionsGenome</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">   </span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filePresent</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">      <span class="n" style="color: #333;">bedRegions</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">,</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">chrFile</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrFile</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">chrFile</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">chrFromFile</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">     <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">chrFile</span><span class="p">,</span> <span class="n" style="color: #333;">chrFromFile</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tokenizer</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">char_separator</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Tokenizer</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">     <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">char_separator</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sep</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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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">     <span class="n" style="color: #333;">Tokenizer</span> <span class="n" style="color: #333;">tokens</span><span class="p">(</span><span class="n" style="color: #333;">chrFromFile</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" 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="LC83" class="line" lang="cpp">     <span class="n" style="color: #333;">Tokenizer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">tokIter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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="LC84" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokIter</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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="LC85" class="line" lang="cpp">       <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">chrName</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tokIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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="LC86" class="line" lang="cpp">       <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_name2id</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">chrName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tid</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>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">         <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokIter</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">tokens</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp">           <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lexical_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</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;">tokIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">           <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lexical_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</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;">tokIter</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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="LC91" class="line" lang="cpp">           <span class="n" style="color: #333;">bedRegions</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="cpp">           <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">intervals</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" 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="LC93" class="line" lang="cpp">         <span class="p">}</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">       <span class="p">}</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp">     <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" 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="LC96" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" 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="LC97" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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="LC98" class="line" lang="cpp">      <span class="n" style="color: #333;">chrFile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">intervals</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TChrIntervals</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">  <span class="n" style="color: #333;">_mergeOverlappingBedEntries</span><span class="p">(</span><span class="n" style="color: #333;">TChrIntervals</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">,</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">citv</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="107" 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="LC107" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">icl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">interval_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TUniqueIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TUniqueIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">interval_type</span> <span class="n" style="color: #333;">TIVal</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp">    <span class="n" style="color: #333;">TUniqueIntervals</span> <span class="n" style="color: #333;">uitv</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Insert intervals</span></span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="n" style="color: #333;">uitv</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">TIVal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">right_open</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Fetch unique intervals</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TUniqueIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">uitv</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">uitv</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lower</span><span class="p">(),</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">upper</span><span class="p">()));</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="d0a709faa909252ae246c0d6c1212099d4cc6343">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#d0a709faa909252ae246c0d6c1212099d4cc6343"><strong>src/cluster.h</strong></a>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TCompEdgeList</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TCo<span class="idiff left">nfig</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">typename</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">TCo</span>mpEdgeList</span><span class="p">></span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp">  <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">TCompEdgeList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SRBamRecord</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">br</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">StructuralVariantRecord</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">wiggle</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp">  <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">TCo<span class="idiff left">nfig</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">c</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">TCo</span>mpEdgeList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SRBamRecord</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">br</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">StructuralVariantRecord</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">wiggle</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TCompEdgeList</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mapped_type</span> <span class="n" style="color: #333;">TEdgeList</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TEdgeList</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">TEdgeRecord</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TEdgeRecord</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TVertexType</span> <span class="n" style="color: #333;">TVertex</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">@@ -285,8 +285,8 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">At least 2</span> split reads?</span></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">clique</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><span class="idiff left">></span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">Enough</span> split reads?</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">clique</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="idiff left"> </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">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">minCliqueSize</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span> <span class="n" style="color: #333;">clique</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="LC291" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">pos2</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span> <span class="n" style="color: #333;">clique</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="LC292" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">svInsLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">inslen</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">clique</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="338" 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="338" 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">@@ -338,7 +338,7 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Clean edge lists</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Search cliques</span></span>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp">        <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">,</span> <span class="n" style="color: #333;">sv</span><span class="p">,</span> <span class="n" style="color: #333;">varisize</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp">        <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ompEdge</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">,</span> <span class="n" style="color: #333;">sv</span><span class="p">,</span> <span class="n" style="color: #333;">varisize</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp">        <span class="n" style="color: #333;">lastConnectedNodeStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastConnectedNode</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp">        <span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp">      <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="409" 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">@@ -409,16 +409,16 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Search cliques</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="cpp">  <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">,</span> <span class="n" style="color: #333;">sv</span><span class="p">,</span> <span class="n" style="color: #333;">varisize</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp">  <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ompEdge</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">,</span> <span class="n" style="color: #333;">sv</span><span class="p">,</span> <span class="n" style="color: #333;">varisize</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="cpp">  <span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TCompEdgeList</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TBamRecord</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TSVs</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TCo<span class="idiff left">nfig</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">typename</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">TCo</span>mpEdgeList</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TBamRecord</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TSVs</span><span class="p">></span></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="cpp">  <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">TCompEdgeList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">TBamRecord</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bamRecord</span><span class="p">,</span> <span class="n" style="color: #333;">TSVs</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp">  <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">TCo<span class="idiff left">nfig</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">c</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">TCo</span>mpEdgeList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">TBamRecord</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bamRecord</span><span class="p">,</span> <span class="n" style="color: #333;">TSVs</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TCompEdgeList</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mapped_type</span> <span class="n" style="color: #333;">TEdgeList</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TEdgeList</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">TEdgeRecord</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"></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">@@ -459,8 +459,9 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">incompatible</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">clique</span><span class="p">.</span><span class="n" style="color: #333;">size</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="p">(</span><span class="n" style="color: #333;">_svSizeCheck</span><span class="p">(</span><span class="n" style="color: #333;">svStart</span><span class="p">,</span> <span class="n" style="color: #333;">svEnd</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">)))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Enough paired-ends</span></span>

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">clique</span><span class="p">.</span><span class="n" style="color: #333;">size</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;">minCliqueSize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">_svSizeCheck</span><span class="p">(</span><span class="n" style="color: #333;">svStart</span><span class="p">,</span> <span class="n" style="color: #333;">svEnd</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">)))</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp">  <span class="n" style="color: #333;">StructuralVariantRecord</span> <span class="n" style="color: #333;">svRec</span><span class="p">;</span></span>

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465

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<td class="diff-line-num new_line" data-linenumber="466" 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">

466

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="cpp">  <span class="n" style="color: #333;">svRec</span><span class="p">.</span><span class="n" style="color: #333;">chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clusterRefID</span><span class="p">;</span></span>

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466

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<td class="diff-line-num new_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp">  <span class="n" style="color: #333;">svRec</span><span class="p">.</span><span class="n" style="color: #333;">chr2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clusterMateRefID</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="520" 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="521" 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">@@ -520,7 +521,7 @@ namespace torali</td>

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<td class="diff-line-num new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bamItIndex</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastConnectedNode</span><span class="p">)</span> <span class="p">{</span></span>

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521

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<td class="diff-line-num new_line" data-linenumber="522" 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">

522

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Clean edge lists</span></span>

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<td class="diff-line-num old_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="523" 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">

523

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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523

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<td class="diff-line-num new_line old" data-linenumber="524" 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="LC523" class="line" lang="cpp">    <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">bamRecord</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="524" 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">

524

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp">    <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ompEdge</span><span class="p">,</span> <span class="n" style="color: #333;">bamRecord</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="524" 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">

524

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<td class="diff-line-num new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp">    <span class="n" style="color: #333;">lastConnectedNodeStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lastConnectedNode</span><span class="p">;</span></span>

</pre>

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525

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<td class="diff-line-num new_line" data-linenumber="526" 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">

526

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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp">    <span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="526" 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">

526

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<td class="diff-line-num new_line" data-linenumber="527" 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">

527

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -591,7 +592,7 @@ namespace torali</td>

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<td class="diff-line-num old_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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<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="cpp">      <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="593" 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">

593

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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="594" 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">

594

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<pre style="margin: 0;"> <span id="LC594" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="594" 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">

594

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<td class="diff-line-num new_line old" data-linenumber="595" 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="LC594" class="line" lang="cpp">      <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">compEdge</span><span class="p">,</span> <span class="n" style="color: #333;">bamRecord</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="595" 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="595" 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">

595

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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp">      <span class="n" style="color: #333;">_searchCliques</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">c</span>ompEdge</span><span class="p">,</span> <span class="n" style="color: #333;">bamRecord</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="595" 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">

595

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<td class="diff-line-num new_line" data-linenumber="596" 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">

596

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<pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp">      <span class="n" style="color: #333;">compEdge</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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596

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<td class="diff-line-num new_line" data-linenumber="597" 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">

597

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<pre style="margin: 0;"> <span id="LC597" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="597" 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">

597

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<td class="diff-line-num new_line" data-linenumber="598" 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">

598

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<pre style="margin: 0;"> <span id="LC598" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="6a965fc172da372b399f988708853bec938e4290">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#6a965fc172da372b399f988708853bec938e4290"><strong>src/cnv.h</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef CNV_H</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define CNV_H</span></span>

</pre>

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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="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/filesystem.hpp></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/multi_array.hpp></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/progress.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/posix_time/posix_time.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/unordered_map.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/algorithm/string.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/tokenizer.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/math/distributions/chi_squared.hpp></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/math/distributions/hypergeometric.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filtering_streambuf.hpp></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filtering_stream.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/copy.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filter/gzip.hpp></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/device/file.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/iostreams/filter/zlib.hpp></span></span>

</pre>

</td>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/faidx.h></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/vcf.h></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/sam.h></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">torali</span></span>

</pre>

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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="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="28" 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">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">CNV</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">chr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="31" 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">

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="32" 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="LC32" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ciposlow</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ciposhigh</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="34" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ciendlow</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ciendhigh</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">srleft</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">srright</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="38" 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="LC38" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nsnps</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cn</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">rdsupport</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">penalty</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mappable</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maf</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">  <span class="n" style="color: #333;">CNV</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cil</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cih</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">cel</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ceh</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">estcn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">sp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">pty</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">chr</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">),</span> <span class="n" style="color: #333;">start</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">end</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">),</span> <span class="n" style="color: #333;">ciposlow</span><span class="p">(</span><span class="n" style="color: #333;">cil</span><span class="p">),</span> <span class="n" style="color: #333;">ciposhigh</span><span class="p">(</span><span class="n" style="color: #333;">cih</span><span class="p">),</span> <span class="n" style="color: #333;">ciendlow</span><span class="p">(</span><span class="n" style="color: #333;">cel</span><span class="p">),</span> <span class="n" style="color: #333;">ciendhigh</span><span class="p">(</span><span class="n" style="color: #333;">ceh</span><span class="p">),</span> <span class="n" style="color: #333;">srleft</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">srright</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">nsnps</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">cn</span><span class="p">(</span><span class="n" style="color: #333;">estcn</span><span class="p">),</span> <span class="n" style="color: #333;">rdsupport</span><span class="p">(</span><span class="n" style="color: #333;">sp</span><span class="p">),</span> <span class="n" style="color: #333;">penalty</span><span class="p">(</span><span class="n" style="color: #333;">pty</span><span class="p">),</span> <span class="n" style="color: #333;">mappable</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">),</span> <span class="n" style="color: #333;">maf</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">  <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TCNV</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SortCNVs</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary_function</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCNV</span><span class="p">,</span> <span class="n" style="color: #333;">TCNV</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="LC50" class="line" lang="cpp">      <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">   <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="n" style="color: #333;">TCNV</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sv1</span><span class="p">,</span> <span class="n" style="color: #333;">TCNV</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sv2</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span><span class="n" style="color: #333;">sv1</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sv2</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">sv1</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">sv2</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sv1</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;">sv2</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="p">((</span><span class="n" style="color: #333;">sv1</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">sv2</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sv1</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;">sv2</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="p">(</span><span class="n" style="color: #333;">sv1</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sv2</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">sv1</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">sv2</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sv1</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;">sv2</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="p">(</span><span class="n" style="color: #333;">sv1</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">sv2</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sv1</span><span class="p">.</span><span class="n" style="color: #333;">penalty</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sv2</span><span class="p">.</span><span class="n" style="color: #333;">penalty</span><span class="p">)));</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp">   <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp">      <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TGcBias</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TCoverage</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">  <span class="n" style="color: #333;">callCNVs</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gcbound</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gcContent</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">uniqContent</span><span class="p">,</span> <span class="n" style="color: #333;">TGcBias</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">TCoverage</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cov</span><span class="p">,</span> <span class="n" style="color: #333;">bam_hdr_t</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// cnv tiling windows, window_offset smallest window, window_size largest window</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">numTiling</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winbound</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;">window_offset</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">winbound</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;">window_size</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">   <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">numTiling</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="67" 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="LC67" class="line" lang="cpp">   <span class="n" style="color: #333;">winbound</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">    <span class="p">}</span></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">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></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">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TCNVec</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCNVec</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TTilingCN</span><span class="p">;</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">

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp">    <span class="n" style="color: #333;">TTilingCN</span> <span class="n" style="color: #333;">cnvec</span><span class="p">(</span><span class="n" style="color: #333;">numTiling</span><span class="p">,</span> <span class="n" style="color: #333;">TCNVec</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" 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="LC74" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numTiling</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">cnvec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">50</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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<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">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 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;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">50</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">covsum</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="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">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winbound</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;">window_offset</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">   <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">tilingPos</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="82" 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="LC82" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="p">((</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</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;">window_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="83" 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="LC83" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">       <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp">       <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">coverage</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">       <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">     <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">     <span class="c1" style="color: #998; font-style: italic;">// Multiple of window size?</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">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pos</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;">winbound</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">fracWindow</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">         <span class="n" style="color: #333;">cnvec</span><span class="p">[</span><span class="n" style="color: #333;">tilingPos</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;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">round</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">100.0</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">       <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">       <span class="n" style="color: #333;">winbound</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="LC94" class="line" lang="cpp">       <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">tilingPos</span><span class="p">;</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp">     <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="96" 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">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp">   <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" 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">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Iterate CNVs</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numTiling</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;">i</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">k</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;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cnvec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cnvec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">','</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" 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">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" 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">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" 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">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" 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">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="dcad3ddfd75218047069bbaa2acab307a0655169">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#dcad3ddfd75218047069bbaa2acab307a0655169"><strong>src/coral.h</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef CORAL_H</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define CORAL_H</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="4" 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">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/icl/split_interval_map.hpp></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/dynamic_bitset.hpp></span></span>

</pre>

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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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/unordered_map.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/posix_time/posix_time.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/gregorian/gregorian.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/math/special_functions/round.hpp></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/progress.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/sam.h></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/faidx.h></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "bed.h"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "scan.h"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gcbias.h"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "cnv.h"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "version.h"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">torali</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">CountDNAConfig</span> <span class="p">{</span></span>

</pre>

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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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">adaptive</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasPanelFile</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasStatsFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasBedFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasScanFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noScanWindowSelection</span><span class="p">;</span></span>

</pre>

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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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nchr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">meanisize</span><span class="p">;</span></span>

</pre>

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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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">window_size</span><span class="p">;</span></span>

</pre>

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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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">window_offset</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">scanWindow</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">minChrLen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">minQual</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="40" 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="LC40" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">mad</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="41" 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="LC41" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">ploidy</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">exclgc</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">uniqueToTotalCovRatio</span><span class="p">;</span></span>

</pre>

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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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fracWindow</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">fragmentUnique</span><span class="p">;</span></span>

</pre>

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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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">controlMaf</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="47" 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">

47

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sampleName</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" 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="LC48" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">outfile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="49" 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="LC49" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">panelfile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="50" 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">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">genome</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">statsFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="52" 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="LC52" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">mapFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="53" 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="LC53" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">bamFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" 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="LC54" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">bedFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="55" 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="LC55" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">scanFile</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="56" 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="LC56" class="line" lang="cpp">  <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="57" 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="LC57" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="58" 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="LC58" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">CountDNAConfigLib</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="59" 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="LC59" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">madCutoff</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">madNormalCutoff</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span> <span class="n" style="color: #333;">genome</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">files</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">  <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">  <span class="n" style="color: #333;">bamCount</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</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;">LibraryInfo</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">li</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GcBias</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gcbound</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Load bam file</span></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">    <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_set_fai_filename</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_idx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_index_load</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">    <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// BED regions</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TChrIntervals</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TRegionsGenome</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">    <span class="n" style="color: #333;">TRegionsGenome</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasBedFile</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_parsePotOverlappingIntervals</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bedFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">(),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasBedFile</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Couldn't parse BED intervals. Do the chromosome names match?"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Parse BAM file</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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="LC86" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ptime</span> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">second_clock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">local_time</span><span class="p">();</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'['</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_simple_string</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">)</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="s" style="color: #d14;">"Count fragments"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">progress_display</span> <span class="n" style="color: #333;">show_progress</span><span class="p">(</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span> <span class="p">);</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Open output files</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filtering_ostream</span> <span class="n" style="color: #333;">dataOut</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="cpp">    <span class="n" style="color: #333;">dataOut</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gzip_compressor</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">    <span class="n" style="color: #333;">dataOut</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file_sink</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">    <span class="n" style="color: #333;">dataOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">start</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">end</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_mappable</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_counts</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"_CN"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filtering_ostream</span> <span class="n" style="color: #333;">panelOut</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasPanelFile</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">      <span class="n" style="color: #333;">panelOut</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gzip_compressor</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">      <span class="n" style="color: #333;">panelOut</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file_sink</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">panelfile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Iterate chromosomes</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp">    <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">faiMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">mapFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="cpp">    <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">faiRef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">show_progress</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" 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">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrNoData</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" 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">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" 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">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Check presence in mappability map</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tname</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" 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">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqlen</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="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="113" 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">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">seqlen</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="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_fetch_seq</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="115" 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">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="116" 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="LC116" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Check presence in reference</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="cpp">      <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="118" 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="LC118" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqlen</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="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">seqlen</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="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" 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="LC120" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_fetch_seq</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="122" 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="LC122" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Get GC and Mappability</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">uniqContent</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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="LC124" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcContent</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</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="125" 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="LC125" class="line" lang="cpp">      <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Mappability map</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">TBitSet</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">  <span class="n" style="color: #333;">TBitSet</span> <span class="n" style="color: #333;">uniq</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="130" 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="LC130" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</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="sc" style="color: #d14;">'C'</span><span class="p">)</span> <span class="n" style="color: #333;">uniq</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// GC map</span></span>

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<td class="diff-line-num new new_line" data-linenumber="134" 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="LC134" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">TBitSet</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="135" 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="LC135" class="line" lang="cpp">  <span class="n" style="color: #333;">TBitSet</span> <span class="n" style="color: #333;">gcref</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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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="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="137" 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">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ref</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="sc" style="color: #d14;">'C'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ref</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="sc" style="color: #d14;">'g'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ref</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="sc" style="color: #d14;">'G'</span><span class="p">))</span> <span class="n" style="color: #333;">gcref</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="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="138" 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="LC138" class="line" lang="cpp">  <span class="p">}</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="140" 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="LC140" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Sum across fragment</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" 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="LC141" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">meanisize</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" 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="LC142" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" 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">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">gcsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" 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="LC144" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="145" 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="LC145" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">halfwin</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="146" 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="LC146" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="cpp">        <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">        <span class="n" style="color: #333;">gcsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcref</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="149" 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="LC149" class="line" lang="cpp">      <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="150" 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="LC150" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp">      <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" 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="LC152" class="line" lang="cpp">      <span class="n" style="color: #333;">gcsum</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">gcref</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="cpp">      <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfwin</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="cpp">      <span class="n" style="color: #333;">gcsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcref</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfwin</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" 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="LC155" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="cpp">    <span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcsum</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="cpp">    <span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">usum</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Coverage track</span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">TCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maxCoverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCount</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="164" 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="LC164" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCount</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TCoverage</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">      <span class="n" style="color: #333;">TCoverage</span> <span class="n" style="color: #333;">cov</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp">      <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Mate map</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="169" 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="LC169" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">TMateMap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="170" 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">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp">  <span class="n" style="color: #333;">TMateMap</span> <span class="n" style="color: #333;">mateMap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="171" 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">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="172" 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="LC172" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Count reads</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="173" 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="LC173" class="line" lang="cpp">  <span class="n" style="color: #333;">hts_itr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_itr_queryi</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="174" 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="LC174" class="line" lang="cpp">  <span class="n" style="color: #333;">bam1_t</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="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="175" 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="LC175" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">lastAlignedPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="176" 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="LC176" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="177" 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="LC177" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">sam_itr_next</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="p">,</span> <span class="n" style="color: #333;">rec</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 class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="178" 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="LC178" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">BAM_FQCFAIL</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FDUP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FUNMAP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FSECONDARY</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FSUPPLEMENTARY</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="179" 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="LC179" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</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;">minQual</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span>        </span>

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<td class="diff-line-num new new_line" data-linenumber="180" 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="LC180" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FMUNMAP</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mtid</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="181" 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="LC181" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="182" 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="LC182" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfAlignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Clean-up the read store for identical alignment positions</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="185" 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="LC185" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastAlignedPos</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp">        <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp">        <span class="n" style="color: #333;">lastAlignedPos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// First read</span></span>

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp">        <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)));</span></span>

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_pair</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp">        <span class="n" style="color: #333;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Second read</span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_pair_mate</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">mateMap</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">hv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mateMap</span><span class="p">.</span><span class="n" style="color: #333;">end</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;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Mate discarded</span></span>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp">        <span class="n" style="color: #333;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// update midpoint</span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">))</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">minNormalISize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">isize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">maxNormalISize</span><span class="p">))</span> <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">isize</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="LC206" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Count fragment</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">midPoint</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">midPoint</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">midPoint</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxCoverage</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="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">midPoint</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp">  <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">  <span class="n" style="color: #333;">hts_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="218" 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="LC218" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="219" 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="LC219" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Call CNVs</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">//callCNVs(c, gcbound, gcContent, uniqContent, gcbias, cov, hdr, refIndex);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="221" 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="LC221" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="223" 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="LC223" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// BED File (target intervals)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="224" 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="LC224" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasBedFile</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="225" 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="LC225" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">adaptive</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="226" 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="LC226" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Merge overlapping BED entries</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="227" 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="LC227" class="line" lang="cpp">    <span class="n" style="color: #333;">TChrIntervals</span> <span class="n" style="color: #333;">citv</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="228" 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="LC228" class="line" lang="cpp">    <span class="n" style="color: #333;">_mergeOverlappingBedEntries</span><span class="p">(</span><span class="n" style="color: #333;">bedRegions</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="n" style="color: #333;">citv</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="229" 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="LC229" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="230" 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="LC230" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Tile merged intervals</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="231" 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="LC231" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="232" 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="LC232" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="233" 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="LC233" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">endOfWindow</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">end</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">endOfWindow</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">      <span class="n" style="color: #333;">endOfWindow</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="p">((</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">end</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;">endOfWindow</span><span class="p">));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp">              <span class="c1" style="color: #998; font-style: italic;">// Special case</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">itNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp">              <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">itNext</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">itNext</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">end</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;">itNext</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp">          <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="p">((</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">endOfWindow</span><span class="p">));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="253" 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="LC253" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp">              <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">              <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">obsexp</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">              <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">coverage</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">              <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">window_size</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp">                <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">obsexp</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_size</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cn</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;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">expcov</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">                <span class="n" style="color: #333;">dataOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">start</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="p">(</span><span class="n" style="color: #333;">pos</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="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;">winlen</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;">count</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;">cn</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// reset</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp">                <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp">                <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp">                <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">                <span class="n" style="color: #333;">winlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_offset</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;">window_size</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">// Move on</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">                  <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</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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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">                  <span class="n" style="color: #333;">endOfWindow</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">                <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">                  <span class="c1" style="color: #998; font-style: italic;">// Rewind</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">sit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="p">((</span><span class="n" style="color: #333;">sit</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">citv</span><span class="p">.</span><span class="n" style="color: #333;">end</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;">endOfWindow</span><span class="p">));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sit</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">sit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">                      <span class="k" style="font-weight: 600;">if</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;">sit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp">                      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="p">((</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sit</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">endOfWindow</span><span class="p">));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="279" 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="LC279" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">k</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">                          <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="282" 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="LC282" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">window_offset</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp">                            <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</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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<td class="diff-line-num new new_line" data-linenumber="284" 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="LC284" class="line" lang="cpp">                            <span class="n" style="color: #333;">winlen</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="285" 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="LC285" class="line" lang="cpp">                            <span class="n" style="color: #333;">endOfWindow</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="286" 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="LC286" class="line" lang="cpp">                          <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp">                        <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="288" 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="LC288" class="line" lang="cpp">                      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp">                    <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="290" 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="LC290" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">                <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp">              <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp">      <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="297" 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="LC297" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Fixed Window Length</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bedRegions</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expcov</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="304" 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="LC304" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">obsexp</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="305" 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="LC305" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp">            <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp">            <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">obsexp</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp">            <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">coverage</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp">          <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">fracWindow</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">          <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">obsexp</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cn</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;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">expcov</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">          <span class="n" style="color: #333;">dataOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">winlen</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;">count</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;">cn</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp">          <span class="n" style="color: #333;">dataOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</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;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Genome-wide</span></span>

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<td class="diff-line-num new new_line" data-linenumber="327" 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="LC327" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">adaptive</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="328" 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="LC328" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="333" 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="LC333" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp">        <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp">        <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">obsexp</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp">        <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">coverage</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">window_size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp">          <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">obsexp</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_size</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cn</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;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">expcov</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp">          <span class="n" style="color: #333;">dataOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">start</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="p">(</span><span class="n" style="color: #333;">pos</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="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;">winlen</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;">count</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;">cn</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// reset</span></span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp">          <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp">          <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp">          <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp">          <span class="n" style="color: #333;">winlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_offset</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;">window_size</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Move on</span></span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp">            <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp">          <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Rewind</span></span>

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<td class="diff-line-num new new_line" data-linenumber="355" 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="LC355" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">k</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp">                <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="358" 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="LC358" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">window_offset</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp">                  <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</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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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp">                  <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp">                  <span class="n" style="color: #333;">winlen</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="362" 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="LC362" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp">                <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp">              <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp">          <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="370" 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="LC370" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Fixed windows (genomic tiling)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="373" 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="LC373" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 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;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">start</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;">window_offset</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="374" 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="LC374" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_size</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">covsum</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="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">

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="377" 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="LC377" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">obsexp</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="378" 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="LC378" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="379" 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="LC379" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</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;">window_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp">            <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp">            <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">obsexp</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="383" 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="LC383" class="line" lang="cpp">            <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</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="384" 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="LC384" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="385" 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="LC385" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">fracWindow</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;">window_size</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="388" 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">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp">          <span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="389" 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">

389

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">obsexp</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_size</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp">          <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cn</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;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">expcov</span><span class="p">;</span></span>

</pre>

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391

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp">          <span class="n" style="color: #333;">dataOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">start</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="p">(</span><span class="n" style="color: #333;">start</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;">window_size</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;">winlen</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;">count</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;">cn</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="395" 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="LC395" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="396" 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="LC396" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="397" 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="LC397" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Panel output?</span></span>

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<td class="diff-line-num new new_line" data-linenumber="398" 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="LC398" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasPanelFile</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// cnv tiling windows</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">smallestWin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">300</span><span class="p">;</span></span>

</pre>

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401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">largestWin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">40000</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">numTiling</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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403

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smallestWin</span><span class="p">;</span></span>

</pre>

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405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">winbound</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">largestWin</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">numTiling</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="407" 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="LC407" class="line" lang="cpp">        <span class="n" style="color: #333;">winbound</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="410" 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="LC410" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cnvec</span><span class="p">(</span><span class="n" style="color: #333;">numTiling</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="411" 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="LC411" class="line" lang="cpp">    <span class="n" style="color: #333;">panelOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"#"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">smallestWin</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">largestWin</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 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;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">50</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</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;">smallestWin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="414" 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="LC414" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">covsum</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="415" 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="LC415" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" 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="LC416" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winlen</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="417" 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="LC417" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">winbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smallestWin</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">tilingPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp">        <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fill</span><span class="p">(</span><span class="n" style="color: #333;">cnvec</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cnvec</span><span class="p">.</span><span class="n" style="color: #333;">end</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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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">validCN</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="p">((</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">largestWin</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</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;">fragmentUnique</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;">meanisize</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp">            <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp">            <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]].</span><span class="n" style="color: #333;">coverage</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">winlen</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp">          <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// Multiple of window size?</span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">pos</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;">winbound</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">winlen</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;">fracWindow</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp">              <span class="n" style="color: #333;">cnvec</span><span class="p">[</span><span class="n" style="color: #333;">tilingPos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">round</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">covsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">expcov</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">100.0</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp">              <span class="n" style="color: #333;">validCN</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="432" 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">

432

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="433" 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">

433

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp">            <span class="n" style="color: #333;">winbound</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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="cpp">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">tilingPos</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="435" 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">

435

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="436" 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">

436

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="437" 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">

437

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">validCN</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="438" 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">

438

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numTiling</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">panelOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cnvec</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="sc" style="color: #d14;">','</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="439" 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">

439

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp">          <span class="n" style="color: #333;">panelOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="440" 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">

440

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">panelOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-2,"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="441" 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">

441

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="442" 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">

442

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="443" 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">

443

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="444" 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">

444

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="445" 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">

445

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="446" 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">

446

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="447" 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="LC447" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// clean-up</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="448" 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">

448

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp">    <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="449" 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="LC449" class="line" lang="cpp">    <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="450" 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">

450

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp">    <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="451" 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">

451

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="452" 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">

452

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp">    <span class="n" style="color: #333;">sam_close</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="453" 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">

453

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp">    <span class="n" style="color: #333;">dataOut</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="454" 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">

454

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp">    <span class="n" style="color: #333;">dataOut</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="455" 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">

455

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasPanelFile</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="456" 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">

456

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp">      <span class="n" style="color: #333;">panelOut</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="457" 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">

457

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp">      <span class="n" style="color: #333;">panelOut</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="458" 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">

458

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="459" 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">

459

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="460" 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">

460

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="461" 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">

461

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="462" 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">

462

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="463" 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">

463

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="464" 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">

464

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">coral</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="465" 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">

465

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp">    <span class="n" style="color: #333;">CountDNAConfig</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="466" 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">

466

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="467" 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="LC467" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Parameter</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="468" 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">

468

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">generic</span><span class="p">(</span><span class="s" style="color: #d14;">"Generic options"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="469" 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">

469

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp">    <span class="n" style="color: #333;">generic</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="470" 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="LC470" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"help,?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"show help message"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="471" 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">

471

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"genome,g"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">genome</span><span class="p">),</span> <span class="s" style="color: #d14;">"genome file"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="472" 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">

472

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"quality,q"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint16_t</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;">minQual</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. mapping quality"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="473" 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">

473

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"mappability,m"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">mapFile</span><span class="p">),</span> <span class="s" style="color: #d14;">"input mappability map"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="474" 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">

474

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"ploidy,y"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint16_t</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;">ploidy</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="s" style="color: #d14;">"baseline ploidy"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="475" 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">

475

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"fragment,e"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">float</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;">fragmentUnique</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mf" style="color: #099;">0.97</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. fragment uniqueness [0,1]"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="476" 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">

476

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"statsfile,s"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">statsFile</span><span class="p">),</span> <span class="s" style="color: #d14;">"gzipped stats output file (optional)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="477" 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">

477

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"outfile,o"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">outfile</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="s" style="color: #d14;">"out.cov.gz"</span><span class="p">),</span> <span class="s" style="color: #d14;">"output file"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="478" 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">

478

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"adaptive-windowing,a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"use mappable bases for window size"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="479" 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">

479

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp">      <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="480" 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="LC480" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="481" 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">

481

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">window</span><span class="p">(</span><span class="s" style="color: #d14;">"Window options"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="482" 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">

482

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp">    <span class="n" style="color: #333;">window</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="483" 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">

483

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"window-size,i"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">window_size</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">10000</span><span class="p">),</span> <span class="s" style="color: #d14;">"window size"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="484" 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="LC484" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"window-offset,j"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">window_offset</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">10000</span><span class="p">),</span> <span class="s" style="color: #d14;">"window offset"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="485" 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">

485

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"bed-intervals,b"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">bedFile</span><span class="p">),</span> <span class="s" style="color: #d14;">"input BED file"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="486" 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">

486

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"fraction-window,k"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">float</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;">fracWindow</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mf" style="color: #099;">0.25</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. callable window fraction [0,1]"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="487" 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">

487

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp">      <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="488" 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="LC488" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="489" 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="LC489" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">gcopt</span><span class="p">(</span><span class="s" style="color: #d14;">"GC options"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="490" 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="LC490" class="line" lang="cpp">    <span class="n" style="color: #333;">gcopt</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="491" 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="LC491" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"scan-window,w"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">scanWindow</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">10000</span><span class="p">),</span> <span class="s" style="color: #d14;">"scanning window size"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="492" 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">

492

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"fraction-unique,f"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">float</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;">uniqueToTotalCovRatio</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mf" style="color: #099;">0.8</span><span class="p">),</span> <span class="s" style="color: #d14;">"uniqueness filter for scan windows [0,1]"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="493" 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">

493

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"scan-regions,r"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">scanFile</span><span class="p">),</span> <span class="s" style="color: #d14;">"scanning regions in BED format"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="494" 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">

494

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"mad-cutoff,d"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint16_t</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;">mad</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">),</span> <span class="s" style="color: #d14;">"median + 3 * mad count cutoff"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="495" 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">

495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"percentile,p"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">float</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;">exclgc</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mf" style="color: #099;">0.0005</span><span class="p">),</span> <span class="s" style="color: #d14;">"excl. extreme GC fraction"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="496" 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">

496

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"no-window-selection,n"</span><span class="p">,</span> <span class="s" style="color: #d14;">"no scan window selection"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="497" 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">

497

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp">      <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="498" 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">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="499" 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">

499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">hidden</span><span class="p">(</span><span class="s" style="color: #d14;">"Hidden options"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="500" 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">

500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp">    <span class="n" style="color: #333;">hidden</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="501" 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">

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"input-file"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">bamFile</span><span class="p">),</span> <span class="s" style="color: #d14;">"input bam file"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="502" 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">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"panelfile,z"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</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;">panelfile</span><span class="p">),</span> <span class="s" style="color: #d14;">"output panel file"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="503" 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">

503

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp">      <span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="504" 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">

504

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="505" 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">

505

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">positional_options_description</span> <span class="n" style="color: #333;">pos_args</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="506" 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">

506

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp">    <span class="n" style="color: #333;">pos_args</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"input-file"</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="507" 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">

507

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="508" 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">

508

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Set the visibility</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="509" 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">

509

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">cmdline_options</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="510" 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">

510

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp">    <span class="n" style="color: #333;">cmdline_options</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">generic</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">window</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">gcopt</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">hidden</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">options_description</span> <span class="n" style="color: #333;">visible_options</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="512" 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="LC512" class="line" lang="cpp">    <span class="n" style="color: #333;">visible_options</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">generic</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">window</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">gcopt</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="513" 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="LC513" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="514" 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="LC514" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Parse command-line</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="515" 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="LC515" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variables_map</span> <span class="n" style="color: #333;">vm</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="516" 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="LC516" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">store</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">command_line_parser</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">).</span><span class="n" style="color: #333;">options</span><span class="p">(</span><span class="n" style="color: #333;">cmdline_options</span><span class="p">).</span><span class="n" style="color: #333;">positional</span><span class="p">(</span><span class="n" style="color: #333;">pos_args</span><span class="p">).</span><span class="n" style="color: #333;">run</span><span class="p">(),</span> <span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="517" 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="LC517" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">notify</span><span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="518" 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="LC518" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check command line arguments</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="520" 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="LC520" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</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;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"input-file"</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;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"genome"</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;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"mappability"</span><span class="p">)))</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="521" 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="LC521" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="522" 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="LC522" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Usage: delly "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [OPTIONS] -g <genome.fa> -m <genome.map> <aligned.bam>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="523" 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="LC523" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">visible_options</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="524" 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="LC524" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="525" 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="LC525" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="526" 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">

526

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="527" 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">

527

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Show cmd</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="528" 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">

528

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ptime</span> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">second_clock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">local_time</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="529" 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">

529

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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'['</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_simple_string</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">)</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="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="530" 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">

530

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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"delly "</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="531" 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">

531

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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 class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">argc</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">argv</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="sc" style="color: #d14;">' '</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="532" 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">

532

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="533" 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">

533

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="534" 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">

534

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Stats file</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="535" 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">

535

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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"statsfile"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasStatsFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="536" 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">

536

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasStatsFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="537" 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">

537

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="538" 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">

538

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// BED intervals</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="539" 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">

539

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"bed-intervals"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasBedFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="540" 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">

540

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasBedFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="541" 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">

541

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="542" 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="LC542" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Scan regions</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="543" 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">

543

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"scan-regions"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="544" 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">

544

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="545" 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">

545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="546" 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="LC546" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Scan window selection</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="547" 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">

547

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"no-window-selection"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">noScanWindowSelection</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="548" 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">

548

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">noScanWindowSelection</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="549" 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">

549

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="550" 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">

550

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Adaptive windowing</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="551" 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">

551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"adaptive-windowing"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">adaptive</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="552" 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">

552

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">adaptive</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="553" 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">

553

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="554" 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">

554

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// CNV mode</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="555" 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">

555

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"panelfile"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasPanelFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="556" 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">

556

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasPanelFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="557" 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">

557

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp">    </span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="558" 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">

558

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check window size</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="559" 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">

559

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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_offset</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;">window_size</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_offset</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;">window_size</span><span class="p">;</span></span>

</pre>

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560

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_size</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="561" 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">

561

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_offset</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">window_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="562" 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">

562

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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="563" 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">

563

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check bam file</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="564" 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">

564

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp">    <span class="n" style="color: #333;">LibraryInfo</span> <span class="n" style="color: #333;">li</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="565" 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">

565

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">is_regular_file</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file_size</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">)))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="566" 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">

566

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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Alignment file is missing: "</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;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="567" 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="LC567" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="568" 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="LC568" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="569" 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">

569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Get scan regions</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="570" 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">

570

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">icl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">interval_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TChrIntervals</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="571" 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">

571

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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">interval_type</span> <span class="n" style="color: #333;">TIVal</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="572" 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="LC572" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TRegionsGenome</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="573" 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">

573

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp">      <span class="n" style="color: #333;">TRegionsGenome</span> <span class="n" style="color: #333;">scanRegions</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="574" 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="LC574" class="line" lang="cpp"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="575" 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">

575

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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Open BAM file</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="576" 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">

576

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp">      <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="577" 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">

577

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="578" 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">

578

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Fail to open file "</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;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="579" 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">

579

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="580" 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">

580

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="581" 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">

581

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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp">      <span class="n" style="color: #333;">hts_idx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_index_load</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="582" 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">

582

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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="583" 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">

583

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam_index_build</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" 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="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="584" 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">

584

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Fail to open index for "</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;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="585" 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">

585

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="586" 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">

586

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="587" 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="LC587" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="588" 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">

588

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp">      <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="589" 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">

589

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="590" 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">

590

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Fail to open header for "</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;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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591

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="592" 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">

592

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="593" 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="LC593" class="line" lang="cpp">      <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">nchr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp">      <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minChrLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">setMinChrLen</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="mf" style="color: #099;">0.95</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="595" 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="LC595" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="596" 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="LC596" class="line" lang="cpp">      <span class="n" style="color: #333;">getSMTag</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">text</span><span class="p">),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">stem</span><span class="p">().</span><span class="n" style="color: #333;">string</span><span class="p">(),</span> <span class="n" style="color: #333;">sampleName</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp">      <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sampleName</span><span class="p">;</span></span>

</pre>

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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="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Check matching chromosome names</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp">      <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">faiRef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp">      <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">faiMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">mapFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mapFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">refFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="604" 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="LC604" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="605" 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="LC605" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tname</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]);</span></span>

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</td>

<td class="diff-line-num new new_line" data-linenumber="606" 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">

606

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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">faidx_has_seq</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()))</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">mapFound</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="607" 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">

607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">faidx_has_seq</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()))</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refFound</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="608" 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">

608

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="609" 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">

609

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: BAM chromosome "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" not present in reference genome!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_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">

610

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp">      <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp">      <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="614" 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">

614

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mapFound</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="615" 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">

615

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Mappability map chromosome naming disagrees with BAM file!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="616" 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">

616

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="617" 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">

617

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="618" 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">

618

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">refFound</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_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">

619

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reference genome chromosome naming disagrees with BAM file!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="620" 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">

620

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="621" 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">

621

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="622" 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">

622

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<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="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Estimate library params</span></span>

</pre>

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</td>

<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="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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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="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_parseBedIntervals</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">scanFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">(),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">scanRegions</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="626" 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">

626

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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: Couldn't parse BED intervals. Do the chromosome names match?"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="627" 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">

627

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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="628" 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">

628

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="629" 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">

629

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" 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">

630

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp">  <span class="n" style="color: #333;">scanRegions</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="631" 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">

631

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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="632" 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">

632

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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp">    <span class="n" style="color: #333;">scanRegions</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">TIVal</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">right_open</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="633" 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">

633

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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="634" 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="LC634" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="635" 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">

635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">LibraryInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSampleLibrary</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="636" 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">

636

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp">      <span class="n" style="color: #333;">TSampleLibrary</span> <span class="n" style="color: #333;">sampleLib</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">LibraryInfo</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="637" 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">

637

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp">      <span class="n" style="color: #333;">CountDNAConfigLib</span> <span class="n" style="color: #333;">dellyConf</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="638" 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="LC638" class="line" lang="cpp">      <span class="n" style="color: #333;">dellyConf</span><span class="p">.</span><span class="n" style="color: #333;">genome</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;">genome</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="639" 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="LC639" class="line" lang="cpp">      <span class="n" style="color: #333;">dellyConf</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="640" 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">

640

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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp">      <span class="n" style="color: #333;">dellyConf</span><span class="p">.</span><span class="n" style="color: #333;">madCutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="641" 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">

641

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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp">      <span class="n" style="color: #333;">dellyConf</span><span class="p">.</span><span class="n" style="color: #333;">madNormalCutoff</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;">mad</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="642" 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">

642

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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp">      <span class="n" style="color: #333;">getLibraryParams</span><span class="p">(</span><span class="n" style="color: #333;">dellyConf</span><span class="p">,</span> <span class="n" style="color: #333;">scanRegions</span><span class="p">,</span> <span class="n" style="color: #333;">sampleLib</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="643" 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">

643

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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp">      <span class="n" style="color: #333;">li</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="644" 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">

644

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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="645" 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="LC645" class="line" lang="cpp">  <span class="n" style="color: #333;">li</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;">250</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="646" 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="LC646" class="line" lang="cpp">  <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="647" 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="LC647" class="line" lang="cpp">  <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">minNormalISize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="648" 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="LC648" class="line" lang="cpp">  <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">maxNormalISize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">400</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="649" 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="LC649" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="650" 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">

650

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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp">      <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">meanisize</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">li</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;">2</span><span class="p">))</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="651" 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="LC651" class="line" lang="cpp">      </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="652" 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="LC652" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp">      <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="654" 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="LC654" class="line" lang="cpp">      <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="655" 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="LC655" class="line" lang="cpp">      <span class="n" style="color: #333;">sam_close</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="657" 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="LC657" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="658" 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="LC658" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// GC bias estimation</span></span>

</pre>

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</td>

<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">

659

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TGCBound</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="660" 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">

660

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp">    <span class="n" style="color: #333;">TGCBound</span> <span class="n" style="color: #333;">gcbound</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="661" 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">

661

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GcBias</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcbias</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">meanisize</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;">GcBias</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="662" 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">

662

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Scan genomic windows</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="664" 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="LC664" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScanWindow</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TWindowCounts</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="665" 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">

665

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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TWindowCounts</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TGenomicWindowCounts</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="666" 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">

666

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp">      <span class="n" style="color: #333;">TGenomicWindowCounts</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">nchr</span><span class="p">,</span> <span class="n" style="color: #333;">TWindowCounts</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="667" 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">

667

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp">      <span class="n" style="color: #333;">scan</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">li</span><span class="p">,</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">);</span></span>

</pre>

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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="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="669" 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="LC669" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Select stable windows</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="670" 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="LC670" class="line" lang="cpp">      <span class="n" style="color: #333;">selectWindows</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="671" 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">

671

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Estimate GC bias</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="LC673" class="line" lang="cpp">      <span class="n" style="color: #333;">gcBias</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">,</span> <span class="n" style="color: #333;">li</span><span class="p">,</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">gcbound</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="674" 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="LC674" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Statistics output</span></span>

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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasStatsFile</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Open stats file</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp">  <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filtering_ostream</span> <span class="n" style="color: #333;">statsOut</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp">  <span class="n" style="color: #333;">statsOut</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gzip_compressor</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp">  <span class="n" style="color: #333;">statsOut</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iostreams</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file_sink</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">statsFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios_base</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp">  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Library Info</span></span>

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp">  <span class="n" style="color: #333;">statsOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"LP</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;">li</span><span class="p">.</span><span class="n" style="color: #333;">rs</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">minNormalISize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">','</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">maxNormalISize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp">  </span>

</pre>

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Scan window summry</span></span>

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp">  <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp">  <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp">  <span class="n" style="color: #333;">statsOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SW</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">chrom</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">start</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">end</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">selected</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">coverage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">uniqcov"</span> <span class="o" style="font-weight: 600;"><<</span>  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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691

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp">      <span class="n" style="color: #333;">statsOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SW</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;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cov</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">uniqcov</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<td class="diff-line-num new 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">

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp">    <span class="p">}</span></span>

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693

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp">  <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp">  <span class="n" style="color: #333;">sam_close</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// GC bias summary</span></span>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp">  <span class="n" style="color: #333;">statsOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"GC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">gcsum</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">sample</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">reference</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">percentileSample</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">percentileReference</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">fractionSample</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">fractionReference</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">obsexp</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">meancoverage"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbias</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">statsOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"GC</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;">i</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sample</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileSample</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileReference</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionSample</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">obsexp</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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700

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp">  <span class="n" style="color: #333;">statsOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BoundsGC</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;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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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="cpp">  <span class="n" style="color: #333;">statsOut</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

</pre>

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702

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp">  <span class="n" style="color: #333;">statsOut</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="703" 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">

703

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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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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="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="705" 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">

705

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp">      </span>

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706

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<pre style="margin: 0;">+<span id="LC706" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Count reads</span></span>

</pre>

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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="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bamCount</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">li</span><span class="p">,</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">gcbound</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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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="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Read counting error!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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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="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="710" 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">

710

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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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711

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<pre style="margin: 0;">+<span id="LC711" class="line" lang="cpp"></span>

</pre>

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712

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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Done</span></span>

</pre>

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713

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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp">    <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">second_clock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">local_time</span><span class="p">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="714" 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">

714

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'['</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_simple_string</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">)</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="s" style="color: #d14;">"Done."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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715

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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"></span>

</pre>

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716

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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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717

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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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718

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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"></span>

</pre>

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719

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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp">  </span>

</pre>

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720

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<pre style="margin: 0;">+<span id="LC720" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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721

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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="e19d274a46472d34d39a42180498e5c30d7e7424">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#e19d274a46472d34d39a42180498e5c30d7e7424"><strong>src/coverage.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" 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">@@ -144,7 +144,7 @@ namespace torali {</td>

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144

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TSVs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TBreakProbes</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TGenomicBpRegion</span><span class="p">></span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp">  <span class="n" style="color: #333;"><span class="idiff left">_generateProbes</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TConfig</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">c</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bam_hdr_t</span></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">hdr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TSVs</span></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">svs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TBreakProbes</span></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">refProbeArr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TBreakProbes</span></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">consProbeArr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TGenomicBpRegion</span></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 right">bpRegion</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">  <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">_generateProbes</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">TConfig</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></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">c</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bam_hdr_t</span></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">hdr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TSVs</span></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">svs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TBreakProbes</span></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">refProbeArr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TBreakProbes</span></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">consProbeArr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TGenomicBpRegion</span></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">bpRegion</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></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 right">svOnChr</span></span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TBreakProbes</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">TProbes</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Preprocess REF and ALT</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" 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="161" 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">@@ -161,7 +161,8 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Iterate all structural variants</span></span>

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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TSVs</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">itSV</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">svs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">itSV</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">svs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">itSV</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itSV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">itSV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">refIndex</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_line" data-linenumber="165" 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="LC164" class="line" lang="cpp">  <span class="n" style="color: #333;">svOnChr</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" 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="165" 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="LC165" class="line" lang="cpp">  </span>

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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Lazy loading of reference sequence</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">seqlen</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="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" 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="292" 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">@@ -291,9 +292,10 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BpRegion</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TBpRegion</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TBpRegion</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TGenomicBpRegion</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp">    <span class="n" style="color: #333;">TGenomicBpRegion</span> <span class="n" style="color: #333;">bpRegion</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">,</span> <span class="n" style="color: #333;">TBpRegion</span><span class="p">());</span></span>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</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;">svOnChr</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Generate probes</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp">    <span class="n" style="color: #333;">_generateProbes</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">refProbeArr</span><span class="p">,</span> <span class="n" style="color: #333;">consProbeArr</span><span class="p">,</span> <span class="n" style="color: #333;">bpRegion</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp">    <span class="n" style="color: #333;">_generateProbes</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">refProbeArr</span><span class="p">,</span> <span class="n" style="color: #333;">consProbeArr</span><span class="p">,</span> <span class="n" style="color: #333;">bpRegion</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">svOnChr</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Debug</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t k = 0; k < 2; ++k) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="340" 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">@@ -340,7 +342,7 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp">  <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">show_progress</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp">      </span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Any SV breakpoints on this chromosome?</span></span>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bpRegion</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">refIndex</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">svOnChr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">refIndex</span></span><span class="p"><span class="idiff right">]</span>)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Check we have mapped reads on this chromosome</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">nodata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="441" 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">@@ -441,6 +443,7 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Fetch all relevant SVs</span></span>

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TBpRegion</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">itBp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lower_bound</span><span class="p">(</span><span class="n" style="color: #333;">bpRegion</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">bpRegion</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">BpRegion</span><span class="p">(</span><span class="n" style="color: #333;">rbegin</span><span class="p">),</span> <span class="n" style="color: #333;">SortBp</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BpRegion</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span><span class="p">(;</span> <span class="p">((</span><span class="n" style="color: #333;">itBp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bpRegion</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bppos</span><span class="p">));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">itBp</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">countMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">countMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</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;">maxGenoReadCount</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// Read spans breakpoint?</span></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">hasSoftClip</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;">hasClip</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">minimumFlankSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">homLeft</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bppos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span>  <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bppos</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;">minimumFlankSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">homRight</span><span class="p">)))</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp">            <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">consProbe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">consProbeArr</span><span class="p">[</span><span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bpPoint</span><span class="p">][</span><span class="n" style="color: #333;">itBp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="535" 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="538" 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">@@ -535,9 +538,9 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp">      <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp">    <span class="p">}</span></span>

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538

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<pre style="margin: 0;">-<span id="LC538" class="line" lang="cpp"><span class="idiff left right">   </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="539" 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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541

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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"></span>

</pre>

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539

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<td class="diff-line-num new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Read-count and spanning annotation</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="540" 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">

540

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<td class="diff-line-num new_line old" data-linenumber="543" 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="LC540" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bpRegion</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">rec</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">core</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mtid</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span>))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="541" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="543" 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">

543

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</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 class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">svOnChr</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">rec</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">core</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mtid</span></span><span class="p"><span class="idiff right">]</span>))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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541

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544

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="542" 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">

542

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<td class="diff-line-num new_line" data-linenumber="545" 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">

545

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Clean-up the read store for identical alignment positions</span></span>

</pre>

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543

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<td class="diff-line-num new_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">

546

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastAlignedPos</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="574" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -574,7 +577,7 @@ namespace torali {</td>

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574

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577

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<pre style="margin: 0;"> <span id="LC577" class="line" lang="cpp">        <span class="n" style="color: #333;">qualitiestra</span><span class="p">[</span><span class="n" style="color: #333;">hv</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>

</pre>

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<td class="diff-line-num 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">

575

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<td class="diff-line-num new_line" data-linenumber="578" 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">

578

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<pre style="margin: 0;"> <span id="LC578" class="line" lang="cpp">        <span class="n" style="color: #333;">cliptra</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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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="579" 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">

579

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC579" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="577" 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">

577

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<td class="diff-line-num new_line old" data-linenumber="580" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC577" class="line" lang="cpp"><span class="idiff left right">       </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="578" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="580" 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">

580

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="578" 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">

578

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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="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Pair quality</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="579" 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">

579

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<td class="diff-line-num new_line" data-linenumber="582" 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">

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pairQuality</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;">minGenoQual</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Low quality pair</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="583" 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">

583

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cpp">      </span>

</pre>

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<br>

</li>

<li id="5d775c4d26336d72c9aaeefa6f42a658ef123ac9">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#5d775c4d26336d72c9aaeefa6f42a658ef123ac9"><strong>src/delly.cpp</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +18,7 @@</td>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "filter.h"</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "merge.h"</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tegua.h"</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "coral.h"</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">torali</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></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="27" 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">@@ -26,13 +27,17 @@ inline void</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">displayUsage</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Usage: delly <command> <arguments>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Commands:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Short-read commands:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"    call         discover and genotype structural variants"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"    lr           long-read SV discovery"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"    merge        merge structural variants across VCF/BCF files and within a single VCF/BCF file"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"    filter       filter somatic or germline structural variants"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Long-read commands:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"    lr           long-read SV discovery"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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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<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="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Read-depth commands:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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="LC39" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"    rd           read-depth normalization"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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="73" 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">@@ -68,6 +73,9 @@ int main(int argc, char **argv) {</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"lr"</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tegua</span><span class="p">(</span><span class="n" style="color: #333;">argc</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;">argv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"rd"</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">coral</span><span class="p">(</span><span class="n" style="color: #333;">argc</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;">argv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="71" 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">

71

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"filter"</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filter</span><span class="p">(</span><span class="n" style="color: #333;">argc</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;">argv</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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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="959a235a0b48a27af0667cc50c53360de917157d">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#959a235a0b48a27af0667cc50c53360de917157d"><strong>src/delly.h</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="54" 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">@@ -54,6 +54,7 @@ namespace torali</td>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">minTraQual</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">minGenoQual</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">madCutoff</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" 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="57" 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="LC57" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">madNormalCutoff</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nchr</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">minimumFlankSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">indelsize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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="62" 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">@@ -61,6 +62,8 @@ namespace torali</td>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">minRefSep</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maxReadSep</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">minClip</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="65" 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="LC65" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maxGenoReadCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">minCliqueSize</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">flankQuality</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasExcludeFile</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasVcfFile</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -196,6 +199,7 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">delly</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp">    <span class="n" style="color: #333;">Config</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp">    <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">isHaplotagged</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp">    <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">madNormalCutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Define generic options</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">svtype</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" 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="218" 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">@@ -214,6 +218,7 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"qual-tra,r"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint16_t</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;">minTraQual</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. PE quality for translocation"</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"mad-cutoff,s"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint16_t</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;">madCutoff</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">9</span><span class="p">),</span> <span class="s" style="color: #d14;">"insert size cutoff, median+s*MAD (deletions only)"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"minclip,c"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">minClip</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">25</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. clipping length"</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="221" 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="LC221" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"min-clique-size,z"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">minCliqueSize</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. PE/SR clique size"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"minrefsep,m"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">minRefSep</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">25</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. reference separation"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"maxreadsep,n"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">maxReadSep</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">),</span> <span class="s" style="color: #d14;">"max. read separation"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp">      <span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="230" 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="235" 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">@@ -230,6 +235,7 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">    <span class="n" style="color: #333;">hidden</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>

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<td class="diff-line-num new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"input-file"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">></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;">files</span><span class="p">),</span> <span class="s" style="color: #d14;">"input file"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"pruning,j"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">graphPruning</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">),</span> <span class="s" style="color: #d14;">"PE graph pruning cutoff"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="233" 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="238" 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="LC238" class="line" lang="cpp">      <span class="p">(</span><span class="s" style="color: #d14;">"max-geno-count,a"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">maxGenoReadCount</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">250</span><span class="p">),</span> <span class="s" style="color: #d14;">"max. number of reads aligned for SR genotyping"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">      <span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">positional_options_description</span> <span class="n" style="color: #333;">pos_args</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" 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="265" 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">@@ -259,6 +265,9 @@ namespace torali</td>

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<td class="diff-line-num old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Dump PE and SR support?</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"dump"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasDumpFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="261" 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">

261

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<td class="diff-line-num new_line" data-linenumber="267" 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">

267

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasDumpFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="262" 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="268" 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">

268

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="262" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="269" 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">

269

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Clique size</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="262" 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="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

270

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minCliqueSize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minCliqueSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="262" 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">

262

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<td class="diff-line-num new_line" data-linenumber="271" 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">

271

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="263" 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">

263

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<td class="diff-line-num new_line" data-linenumber="272" 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">

272

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check quality cuts</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="264" 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">

264

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<td class="diff-line-num new_line" data-linenumber="273" 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">

273

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minMapQual</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;">minTraQual</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minTraQual</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;">minMapQual</span><span class="p">;</span></span>

</pre>

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</table>

<br>

</li>

<li id="bd5bcc3550f5a1f8c55a54de46b962722805f66a">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#bd5bcc3550f5a1f8c55a54de46b962722805f66a"><strong>src/gcbias.h</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="0" 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="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef GCBIAS_H</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define GCBIAS_H</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/unordered_map.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/program_options/cmdline.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="6" 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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/program_options/options_description.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/program_options/parsers.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/program_options/variables_map.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/posix_time/posix_time.hpp></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/gregorian/gregorian.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/tuple/tuple.hpp></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/filesystem.hpp></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/progress.hpp></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/dynamic_bitset.hpp></span></span>

</pre>

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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="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/faidx.h></span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/sam.h></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/vcf.h></span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "scan.h"</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util.h"</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">torali</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">GcBias</span> <span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">sample</span><span class="p">;</span></span>

</pre>

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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="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">reference</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">fractionSample</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">fractionReference</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">percentileSample</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">percentileReference</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">obsexp</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</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="34" 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="LC34" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp">    <span class="n" style="color: #333;">GcBias</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">reference</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">fractionSample</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">fractionReference</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">percentileSample</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">percentileReference</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">obsexp</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">coverage</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">  <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">  <span class="n" style="color: #333;">gcBound</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GcBias</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">gcbias</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcbias</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="LC43" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbias</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileSample</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;">exclgc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileReference</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;">exclgc</span><span class="p">))</span> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileSample</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;">exclgc</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="p">(</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileReference</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;">exclgc</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upperBound</span><span class="p">)</span> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">upperBound</span><span class="p">)</span> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lowerBound</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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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    // Adjust total</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    uint64_t totalSampleCount = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    uint64_t totalReferenceCount = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    for(uint32_t i = lowerBound + 1; i < upperBound; ++i) {</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">      totalSampleCount += gcbias[i].sample;</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">      totalReferenceCount += gcbias[i].reference;</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    }    </span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    // Re-estimate observed/expected</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    for(uint32_t i = lowerBound + 1; i < upperBound; ++i) {</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">      gcbias[i].fractionSample = (double) gcbias[i].sample / (double) totalSampleCount;</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">      gcbias[i].fractionReference = (double) gcbias[i].reference / (double) totalReferenceCount;</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">      gcbias[i].obsexp = 1;</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">      if (gcbias[i].fractionReference > 0) gcbias[i].obsexp = gcbias[i].fractionSample / gcbias[i].fractionReference;</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    }</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    */</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">  <span class="p">}</span></span>

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69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">double</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">  <span class="n" style="color: #333;">getPercentIdentity</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Sequence</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sequence</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">    <span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_seq</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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 class="p">;</span> <span class="n" style="color: #333;">i</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">sequence</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="s" style="color: #d14;">"=ACMGRSVTWYHKDBN"</span><span class="p">[</span><span class="n" style="color: #333;">bam_seqi</span><span class="p">(</span><span class="n" style="color: #333;">seqptr</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">)];</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Reference slice</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">refslice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_upper_copy</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">seq</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lastAlignedPosition</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp">         </span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Percent identity</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">rp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// reference pointer</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// sequence pointer</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_cigar</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">matchCount</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="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">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">mismatchCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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 class="p">;</span> <span class="n" style="color: #333;">i</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CMATCH</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CEQUAL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CDIFF</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">   <span class="c1" style="color: #998; font-style: italic;">// match or mismatch</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">k</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="n" style="color: #333;">sp</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">refslice</span><span class="p">[</span><span class="n" style="color: #333;">rp</span><span class="p">])</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">matchCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">mismatchCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">     <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sp</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp">     <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">rp</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp">   <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CDEL</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">   <span class="n" style="color: #333;">mismatchCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp">   <span class="n" style="color: #333;">rp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CINS</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">  <span class="n" style="color: #333;">mismatchCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">  <span class="n" style="color: #333;">sp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CSOFT_CLIP</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp">  <span class="n" style="color: #333;">sp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CHARD_CLIP</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" 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">

106

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam_cigar_op</span><span class="p">(</span><span class="n" style="color: #333;">cigar</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;">BAM_CREF_SKIP</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" 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">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp">  <span class="n" style="color: #333;">mismatchCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" 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="LC108" class="line" lang="cpp">  <span class="n" style="color: #333;">rp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bam_cigar_oplen</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" 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="LC109" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unknown Cigar options"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="112" 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">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">matchCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mismatchCount</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;">percid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">matchCount</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">matchCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mismatchCount</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">percid</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TGCBound</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">  <span class="n" style="color: #333;">gcBias</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScanWindow</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">,</span> <span class="n" style="color: #333;">LibraryInfo</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">li</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GcBias</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">TGCBound</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gcbound</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Load bam file</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp">    <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_set_fai_filename</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_idx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_index_load</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp">    <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="129" 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="LC129" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="130" 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="LC130" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Parse bam (contig by contig)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="131" 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="LC131" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ptime</span> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">second_clock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">local_time</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="132" 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="LC132" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'['</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_simple_string</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">)</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="s" style="color: #d14;">"Estimate GC bias"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">progress_display</span> <span class="n" style="color: #333;">show_progress</span><span class="p">(</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="135" 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="LC135" class="line" lang="cpp">    <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">faiMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">mapFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp">    <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">faiRef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="138" 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="LC138" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">show_progress</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" 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="LC141" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Bin map</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" 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="LC142" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">binMap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" 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="LC143" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" 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="LC144" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Fill bin map</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" 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="LC145" class="line" lang="cpp">  <span class="n" style="color: #333;">binMap</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="n" style="color: #333;">LAST_BIN</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" 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="LC146" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bin</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;">bin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">LAST_BIN</span><span class="p">));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bin</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="n" style="color: #333;">binMap</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bin</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="149" 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="LC149" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="150" 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="LC150" class="line" lang="cpp">      </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" 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="LC151" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Check presence in mappability map</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="152" 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="LC152" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tname</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqlen</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="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" 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="LC155" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">seqlen</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="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_fetch_seq</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" 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="LC158" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Check presence in reference</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">      <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqlen</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="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">seqlen</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="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" 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="LC162" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_fetch_seq</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="164" 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="LC164" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Get GC and Mappability</span></span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">uniqContent</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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="LC166" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gcContent</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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="LC167" class="line" lang="cpp">      <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Mappability map</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">TBitSet</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="170" 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="LC170" class="line" lang="cpp">  <span class="n" style="color: #333;">TBitSet</span> <span class="n" style="color: #333;">uniq</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="172" 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="LC172" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</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="sc" style="color: #d14;">'C'</span><span class="p">)</span> <span class="n" style="color: #333;">uniq</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="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"></span>

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<td class="diff-line-num new new_line" data-linenumber="175" 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="LC175" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// GC map</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="176" 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="LC176" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">TBitSet</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="177" 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="LC177" class="line" lang="cpp">  <span class="n" style="color: #333;">TBitSet</span> <span class="n" style="color: #333;">gcref</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="178" 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="LC178" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ref</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ref</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="sc" style="color: #d14;">'C'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ref</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="sc" style="color: #d14;">'g'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ref</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="sc" style="color: #d14;">'G'</span><span class="p">))</span> <span class="n" style="color: #333;">gcref</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Sum across fragments</span></span>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">meanisize</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="LC184" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">usum</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="185" 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="LC185" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">gcsum</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="186" 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="LC186" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">halfwin</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">        <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">        <span class="n" style="color: #333;">gcsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcref</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" 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="LC192" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="193" 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="LC193" class="line" lang="cpp">      <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="194" 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">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp">      <span class="n" style="color: #333;">gcsum</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">gcref</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp">      <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfwin</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp">      <span class="n" style="color: #333;">gcsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcref</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfwin</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="198" 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="LC198" class="line" lang="cpp">    <span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcsum</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="199" 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="LC199" class="line" lang="cpp">    <span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">usum</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Coverage track</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">TCount</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="205" 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="LC205" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maxCoverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCount</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCount</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TCoverage</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp">      <span class="n" style="color: #333;">TCoverage</span> <span class="n" style="color: #333;">cov</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">      </span>

</pre>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Mate map</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">TMateMap</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp">      <span class="n" style="color: #333;">TMateMap</span> <span class="n" style="color: #333;">mateMap</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Parse BAM</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp">      <span class="n" style="color: #333;">hts_itr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_itr_queryi</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]);</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">      <span class="n" style="color: #333;">bam1_t</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="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">lastAlignedPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">sam_itr_next</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="p">,</span> <span class="n" style="color: #333;">rec</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 class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">BAM_FSECONDARY</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FQCFAIL</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FDUP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FSUPPLEMENTARY</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FUNMAP</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FMUNMAP</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mtid</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</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;">minQual</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfAlignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Clean-up the read store for identical alignment positions</span></span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastAlignedPos</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp">      <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp">      <span class="n" style="color: #333;">lastAlignedPos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Process pair</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// First read</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">      <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_pair</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">      <span class="n" style="color: #333;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="237" 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="LC237" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Second read</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_pair_mate</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="241" 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="LC241" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">mateMap</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">hv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mateMap</span><span class="p">.</span><span class="n" style="color: #333;">end</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;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Mate discarded</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">      <span class="n" style="color: #333;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Insert size filter</span></span>

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<td class="diff-line-num new new_line" data-linenumber="246" 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="LC246" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">))</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="247" 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="LC247" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">minNormalISize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">isize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">maxNormalISize</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="248" 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="LC248" class="line" lang="cpp">      <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">isize</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="LC249" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FREVERSE</span><span class="p">)</span> <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</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;">meanisize</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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<td class="diff-line-num new new_line" data-linenumber="251" 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="LC251" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">meanisize</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="LC252" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Count fragment</span></span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">midPoint</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">midPoint</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">midPoint</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxCoverage</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="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">midPoint</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">      <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="259" 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="LC259" class="line" lang="cpp">      <span class="n" style="color: #333;">hts_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="260" 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="LC260" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="262" 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="LC262" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Summarize GC coverage for this chromosome</span></span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">fragmentUnique</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;">meanisize</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Valid bin?</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_findScanWindow</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="n" style="color: #333;">binMap</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">select</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]].</span><span class="n" style="color: #333;">reference</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]].</span><span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">gcContent</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]].</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cov</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Normalize GC coverage</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="278" 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="LC278" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbias</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span><span class="p">)</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Determine percentiles</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">totalSampleCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">totalReferenceCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbias</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp">      <span class="n" style="color: #333;">totalSampleCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sample</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp">      <span class="n" style="color: #333;">totalReferenceCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cumSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cumReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbias</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp">      <span class="n" style="color: #333;">cumSample</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sample</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp">      <span class="n" style="color: #333;">cumReference</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalSampleCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalReferenceCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">cumSample</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalSampleCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">cumReference</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalReferenceCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">obsexp</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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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionSample</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Estimate correctable GC range</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp">    <span class="n" style="color: #333;">gcbound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcBound</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">gcbias</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Adjust correction to the callable range</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">    <span class="n" style="color: #333;">totalSampleCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp">    <span class="n" style="color: #333;">totalReferenceCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp">      <span class="n" style="color: #333;">totalSampleCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sample</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp">      <span class="n" style="color: #333;">totalReferenceCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp">    <span class="n" style="color: #333;">cumSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp">    <span class="n" style="color: #333;">cumReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Re-initialize</span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbias</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="319" 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="LC319" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">obsexp</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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<td class="diff-line-num new new_line" data-linenumber="322" 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="LC322" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">first</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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gcbound</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp">      <span class="n" style="color: #333;">cumSample</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sample</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp">      <span class="n" style="color: #333;">cumReference</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="326" 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="LC326" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalSampleCount</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reference</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalReferenceCount</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">cumSample</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalSampleCount</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">percentileReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">cumReference</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">totalReferenceCount</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp">      <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">obsexp</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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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</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;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">obsexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionSample</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gcbias</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">fractionReference</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp">    <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">faiRef</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp">    <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp">    <span class="n" style="color: #333;">sam_close</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp">    <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="836bf99511b7d355c156c4bd68f24fd0b7ce69c9">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#836bf99511b7d355c156c4bd68f24fd0b7ce69c9"><strong>src/genotype.h</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">@@ -335,6 +335,9 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Genotype all SVs covered by this read</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TSVSeqHit</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">git</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genoMap</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">git</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">genoMap</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">git</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">svid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">git</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maxGenoReadCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">500</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">jctMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">jctMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">maxGenoReadCount</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp">        </span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">rpHit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">git</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">spHit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">git</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp">      </span>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Compute alignment to alternative haplotype</span></span>

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp">        <span class="n" style="color: #333;">TAlign</span> <span class="n" style="color: #333;">alignAlt</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp">        <span class="n" style="color: #333;">DnaScore</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="n" style="color: #333;">simple</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">aliscore</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">aliscore</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">aliscore</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">aliscore</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp">        <span class="n" style="color: #333;">AlignConfig</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">semiglobal</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreAlt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">needle</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">gbp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">svid</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">subseq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alignAlt</span></span><span class="p">,</span> <span class="n" style="color: #333;">semiglobal</span><span class="p">,</span> <span class="n" style="color: #333;">simple</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreAlt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">needle<span class="idiff left">Banded</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gbp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">svid</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">subseq</span></span><span class="p">,</span> <span class="n" style="color: #333;">semiglobal</span><span class="p">,</span> <span class="n" style="color: #333;">simple</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp">        <span class="n" style="color: #333;">scoreAlt</span> <span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">flankQuality</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gbp</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="mf" style="color: #099;">1.0</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;">flankQuality</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gbp</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp">      </span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Compute alignment to reference haplotype</span></span>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp">        <span class="n" style="color: #333;">TAlign</span> <span class="n" style="color: #333;">alignRef</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreRef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">needle</span><span class="p">(</span><span class="n" style="color: #333;">gbp</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">subseq</span><span class="p">,</span> <span class="n" style="color: #333;">alignRef</span><span class="p">,</span> <span class="n" style="color: #333;">semiglobal</span><span class="p">,</span> <span class="n" style="color: #333;">simple</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreRef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">needleBanded</span><span class="p">(</span><span class="n" style="color: #333;">gbp</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">subseq</span><span class="p">,</span> <span class="n" style="color: #333;">semiglobal</span><span class="p">,</span> <span class="n" style="color: #333;">simple</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp">        <span class="n" style="color: #333;">scoreRef</span> <span class="o" style="font-weight: 600;">/=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">flankQuality</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gbp</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="mf" style="color: #099;">1.0</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;">flankQuality</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gbp</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">simple</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Debug alignment to REF and ALT</span></span>

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "svid:" << svid << ",seqbp:" << spHit << ",readlen:" << readlen << ",reverse:" << (int32_t) (rec->core.flag & BAM_FREVERSE) << ",alt:" << scoreAlt << ",ref:" << scoreRef << std::endl;</span></span>

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t i = 0; i< alignAlt.shape()[0]; ++i) {</span></span>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t j = 0; j< alignAlt.shape()[1]; ++j) std::cerr << alignAlt[i][j];</span></span>

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cerr << std::endl;</span></span>

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//}</span></span>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t i = 0; i< alignRef.shape()[0]; ++i) {</span></span>

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t j = 0; j< alignRef.shape()[1]; ++j) std::cerr << alignRef[i][j];</span></span>

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<td class="diff-line-num new_line old" data-linenumber="382" 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="LC389" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//std::cerr << std::endl;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="390" 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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<td class="diff-line-num new_line old" data-linenumber="382" 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="LC390" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="391" 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">

391

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<td class="diff-line-num new_line old" data-linenumber="382" 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="LC391" class="line" lang="cpp">        </span>

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<td class="diff-line-num old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Any confident alignment?</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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">

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">scoreRef</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="p">(</span><span class="n" style="color: #333;">scoreAlt</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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">

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scoreRef</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">scoreAlt</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="398" 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="388" 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">@@ -398,7 +388,7 @@ namespace torali</td>

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<td class="diff-line-num old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp">              <span class="n" style="color: #333;">quality</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp">              <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qualptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_qual</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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 class="p">;</span> <span class="n" style="color: #333;">i</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">quality</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;">qualptr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<td class="diff-line-num old old_line" data-linenumber="401" 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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<td class="diff-line-num new_line old" data-linenumber="391" 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="LC401" class="line" lang="cpp">              <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">rq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">_getAlignmentQual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">alignRef</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">quality</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="402" 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="391" 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="LC391" class="line" lang="cpp">              <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">rq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">scoreRef</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">35</span></span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rq</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;">minGenoQual</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hpptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"HP"</span><span class="p">);</span></span>

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<td class="diff-line-num 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">

404

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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp">                <span class="n" style="color: #333;">jctMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">)</span> <span class="n" style="color: #333;">std</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;">rq</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">));</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="415" 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="405" 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">@@ -415,7 +405,7 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp">            <span class="n" style="color: #333;">quality</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qualptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_qual</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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 class="p">;</span> <span class="n" style="color: #333;">i</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">quality</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;">qualptr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<td class="diff-line-num old old_line" data-linenumber="418" 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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<td class="diff-line-num new_line old" data-linenumber="408" 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="LC418" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">aq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">_getAlignmentQual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">alignAlt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">quality</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="419" 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="LC408" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">aq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">scoreAlt</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">35</span></span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">aq</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;">minGenoQual</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp">              <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hpptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"HP"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasDumpFile</span><span class="p">)</span> <span class="p">{</span></span>

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<br>

</li>

<li id="88ce703739571701e1144b45c8b9e7a2ef9dd1c1">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#88ce703739571701e1144b45c8b9e7a2ef9dd1c1"><strong>src/merge.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,6 +131,7 @@ void _fillIntervalMap(MergeConfig const& c, TGenomeIntervals& iScore, TContigMap</td>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">inslenVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_get_info_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"INSLEN"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">inslen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ninslen</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 class="n" style="color: #333;">inslenVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inslen</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">inslenVal</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;">minsize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">inslenVal</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;">maxsize</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="134" 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="LC134" class="line" lang="cpp">  <span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">inslenVal</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// To enable reciprocal overlap</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Other intra-chr SV</span></span>

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136

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">svStart</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;">minsize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">svStart</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;">maxsize</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="391" 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="392" 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">@@ -391,6 +392,7 @@ void _outputSelectedIntervals(MergeConfig& c, TGenomeIntervals const& iSelected,</td>

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391

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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_get_info_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">],</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">],</span> <span class="s" style="color: #d14;">"END"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">svend</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nsvend</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 class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">svend</span><span class="p">;</span></span>

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392

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<td class="diff-line-num new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">inslenVal</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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393

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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_get_info_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">],</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">],</span> <span class="s" style="color: #d14;">"INSLEN"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">inslen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ninslen</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 class="n" style="color: #333;">inslenVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inslen</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="394" 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="395" 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">

395

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">recsvt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">inslenVal</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// To enable reciprocal overlap</span></span>

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<td class="diff-line-num new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Parse INFO fields</span></span>

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<td class="diff-line-num new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"BND"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">inslenVal</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;">minsize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">inslenVal</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;">maxsize</span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"BND"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">svStart</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;">minsize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">svStart</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;">maxsize</span><span class="p">)))</span> <span class="p">{</span></span>

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</li>

<li id="961fb7e93e491fbba61e895bde9438ca23a92e42">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#961fb7e93e491fbba61e895bde9438ca23a92e42"><strong>src/modvcf.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="651" 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="651" 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">@@ -651,8 +651,10 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord> const& svs, TJ</td>

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651

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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gqval</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="n" style="color: #333;">ftarr</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"LowQual"</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="652" 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">

652

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<td class="diff-line-num new_line" data-linenumber="652" 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">

652

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ftarr</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PASS"</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp">      <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">svIter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mapq</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC655" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">qvalout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">svIter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mapq</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qvalout</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;">qvalout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">qvalout</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10000</span><span class="p">)</span> <span class="n" style="color: #333;">qvalout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp">      <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qvalout</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp">      </span>

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<pre style="margin: 0;"> <span id="LC659" class="line" lang="cpp">      <span class="n" style="color: #333;">bcf_update_genotypes</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="n" style="color: #333;">gts</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_hdr_nsamples</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">)</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="LC660" class="line" lang="cpp">      <span class="n" style="color: #333;">bcf_update_format_float</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"GL"</span><span class="p">,</span>  <span class="n" style="color: #333;">gls</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_hdr_nsamples</span><span class="p">(</span><span class="n" style="color: #333;">hdr</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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<br>

</li>

<li id="3c321c0c9f85ac1d870308c56630d8d53e324018">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#3c321c0c9f85ac1d870308c56630d8d53e324018"><strong>src/needle.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" 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="268" 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">@@ -268,6 +268,58 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Score</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="LC271" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="LC272" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TAlignConfig</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TScoreObject</span><span class="p">></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="275" 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">

275

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">  <span class="n" style="color: #333;">needleBanded</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s2</span><span class="p">,</span> <span class="n" style="color: #333;">TAlignConfig</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ac</span><span class="p">,</span> <span class="n" style="color: #333;">TScoreObject</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sc</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="276" 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">

276

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

277

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TScoreObject</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TValue</span> <span class="n" style="color: #333;">TScoreValue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="278" 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="LC278" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="279" 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">

279

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// DP Matrix</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s1</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="281" 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="LC281" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s2</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="282" 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">

282

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">band</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="283" 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="LC283" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">lowBand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="284" 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="LC284" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">highBand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">band</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="285" 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="LC285" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="n" style="color: #333;">highBand</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="286" 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="LC286" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">lowBand</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="287" 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="LC287" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TScoreValue</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;">n</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="288" 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="LC288" class="line" lang="cpp">    <span class="n" style="color: #333;">TScoreValue</span> <span class="n" style="color: #333;">prevsub</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="289" 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="LC289" class="line" lang="cpp">    <span class="n" style="color: #333;">TScoreValue</span> <span class="n" style="color: #333;">prevprevsub</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="290" 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="LC290" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="291" 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="LC291" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// DP</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="292" 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="LC292" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">row</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;">row</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">m</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">row</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="293" 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="LC293" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">max</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lowBand</span><span class="p">);</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">std</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;">n</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">highBand</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="294" 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="LC294" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Initialization</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="295" 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="LC295" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">col</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="296" 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="LC296" class="line" lang="cpp">    <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" 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="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="297" 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="LC297" class="line" lang="cpp">    <span class="n" style="color: #333;">prevsub</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="298" 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="LC298" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">row</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="299" 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="LC299" class="line" lang="cpp">    <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_horizontalGap</span><span class="p">(</span><span class="n" style="color: #333;">ac</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">ge</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="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">

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">col</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="301" 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="LC301" class="line" lang="cpp">    <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_verticalGap</span><span class="p">(</span><span class="n" style="color: #333;">ac</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">ge</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="302" 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="LC302" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">row</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">prevsub</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" 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="303" 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="LC303" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">prevsub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_verticalGap</span><span class="p">(</span><span class="n" style="color: #333;">ac</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">row</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="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">ge</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="304" 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="LC304" class="line" lang="cpp">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Recursion</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">    <span class="n" style="color: #333;">prevprevsub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prevsub</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="307" 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="LC307" class="line" lang="cpp">    <span class="n" style="color: #333;">prevsub</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;">col</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="308" 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="LC308" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lowBand</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="309" 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="LC309" class="line" lang="cpp">      <span class="n" style="color: #333;">prevprevsub</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;">col</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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<td class="diff-line-num new new_line" data-linenumber="310" 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="LC310" class="line" lang="cpp">      <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">col</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="n" style="color: #333;">DELLY_OUTOFBAND</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="311" 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="LC311" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">highBand</span><span class="p">)</span> <span class="n" style="color: #333;">prevsub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DELLY_OUTOFBAND</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp">    <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">col</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</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;">std</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;">prevprevsub</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="n" style="color: #333;">row</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="n" style="color: #333;">s2</span><span class="p">[</span><span class="n" style="color: #333;">col</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="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">mismatch</span><span class="p">),</span> <span class="n" style="color: #333;">prevsub</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_verticalGap</span><span class="p">(</span><span class="n" style="color: #333;">ac</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">ge</span><span class="p">)),</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">col</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="n" style="color: #333;">_horizontalGap</span><span class="p">(</span><span class="n" style="color: #333;">ac</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">ge</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Score</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"></span>

</pre>

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271

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp">  </span>

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<td class="diff-line-num old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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324

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TAlign1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TAlign2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TAlign</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TAlignConfig</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TScoreObject</span><span class="p">></span></span>

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273

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325

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>

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<br>

</li>

<li id="5165b8164503f1ee0f58727e13103d7a1f7b025b">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#5165b8164503f1ee0f58727e13103d7a1f7b025b"><strong>src/scan.h</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef SCAN_H</span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define SCAN_H</span></span>

</pre>

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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="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/icl/split_interval_map.hpp></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/dynamic_bitset.hpp></span></span>

</pre>

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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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/unordered_map.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/posix_time/posix_time.hpp></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="10" 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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/date_time/gregorian/gregorian.hpp></span></span>

</pre>

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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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/progress.hpp></span></span>

</pre>

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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="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/sam.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "version.h"</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util.h"</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">torali</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">ScanWindow</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">select</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">end</span><span class="p">;</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">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cov</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">uniqcov</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">    <span class="n" style="color: #333;">ScanWindow</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">select</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">start</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">end</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">cov</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">uniqcov</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="30" 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="LC30" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">explicit</span> <span class="n" style="color: #333;">ScanWindow</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">select</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">start</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">),</span> <span class="n" style="color: #333;">end</span><span class="p">(</span><span class="n" style="color: #333;">s</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;">cov</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">uniqcov</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="cpp">  <span class="p">};</span></span>

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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="cpp"></span>

</pre>

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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="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TScanWindow</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SortScanWindow</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary_function</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TScanWindow</span><span class="p">,</span> <span class="n" style="color: #333;">TScanWindow</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="LC35" class="line" lang="cpp">  <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp">    <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()(</span><span class="n" style="color: #333;">TScanWindow</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sw1</span><span class="p">,</span> <span class="n" style="color: #333;">TScanWindow</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sw2</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span><span class="n" style="color: #333;">sw1</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;">sw2</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="p">((</span><span class="n" style="color: #333;">sw1</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;">sw2</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="p">(</span><span class="n" style="color: #333;">sw1</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sw2</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)));</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">  <span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">></span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">  <span class="n" style="color: #333;">_findScanWindow</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">reflen</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">binMap</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">midPoint</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">binMap</span><span class="p">[</span><span class="n" style="color: #333;">midPoint</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">LAST_BIN</span><span class="p">)</span> <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 class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">binMap</span><span class="p">[</span><span class="n" style="color: #333;">midPoint</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">midPoint</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;">scanWindow</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allbins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reflen</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;">scanWindow</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">allbins</span><span class="p">)</span> <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 class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bin</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp">    <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 class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">  <span class="n" style="color: #333;">estCountBounds</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScanWindow</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">all</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span><span class="p">)</span> <span class="n" style="color: #333;">all</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cov</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="66" 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="LC66" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">all</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">all</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="67" 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="LC67" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all</span><span class="p">[</span><span class="n" style="color: #333;">all</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">absdev</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">all</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">absdev</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">all</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="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">median</span><span class="p">));</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">absdev</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">absdev</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">absdev</span><span class="p">[</span><span class="n" style="color: #333;">absdev</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">];</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">median</span><span class="p">)</span> <span class="n" style="color: #333;">lowerBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mad</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" 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="LC74" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">upperBound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mad</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">upperBound</span><span class="p">);</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">></span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp">  <span class="n" style="color: #333;">scan</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</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;">LibraryInfo</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">li</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScanWindow</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Load bam file</span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp">    <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_set_fai_filename</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_idx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_index_load</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp">    <span class="n" style="color: #333;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Pre-defined scanning windows</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">icl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">interval_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TChrIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TRegionsGenome</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp">      <span class="n" style="color: #333;">TRegionsGenome</span> <span class="n" style="color: #333;">scanRegions</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">_parseBedIntervals</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">scanFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">(),</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">scanRegions</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp">   <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: Couldn't parse BED intervals. Do the chromosome names match?"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp">      <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="96" 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="LC96" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="97" 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">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TChrIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scanRegions</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">scanRegions</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">it</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp">     <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">upper</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="99" 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="LC99" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lower</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 class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">upper</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp">        <span class="n" style="color: #333;">ScanWindow</span> <span class="n" style="color: #333;">sw</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp">        <span class="n" style="color: #333;">sw</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;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lower</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp">        <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">upper</span><span class="p">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="103" 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="LC103" class="line" lang="cpp">        <span class="n" style="color: #333;">sw</span><span class="p">.</span><span class="n" style="color: #333;">select</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="cpp">        <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">sw</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" 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="LC106" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" 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="LC107" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="108" 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="LC108" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Sort scan windows</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" 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="LC109" class="line" lang="cpp">  <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">SortScanWindow</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScanWindow</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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="LC111" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Parse BAM file</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ptime</span> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">second_clock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">local_time</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'['</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">posix_time</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_simple_string</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">)</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="s" style="color: #d14;">"Scanning Windows"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">progress_display</span> <span class="n" style="color: #333;">show_progress</span><span class="p">(</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Iterate chromosomes</span></span>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">totalCov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp">    <span class="n" style="color: #333;">faidx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">faiMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fai_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">mapFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">show_progress</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">chrNoData</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Exclude small chromosomes</span></span>

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<td class="diff-line-num new new_line" data-linenumber="125" 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="LC125" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">minChrLen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">totalCov</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1000000</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Exclude sex chromosomes</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"chrX"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"chrY"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"X"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Y"</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Check presence in mappability map</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tname</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<td class="diff-line-num new new_line" data-linenumber="132" 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="LC132" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqlen</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="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="133" 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="LC133" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">seqlen</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="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">faidx_fetch_seq</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">faidx_seq_len</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">,</span> <span class="n" style="color: #333;">tname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">()),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Get Mappability</span></span>

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<td class="diff-line-num new new_line" data-linenumber="137" 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="LC137" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">uniqContent</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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="LC138" class="line" lang="cpp">      <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Mappability map</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">dynamic_bitset</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">TBitSet</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" 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="LC141" class="line" lang="cpp">  <span class="n" style="color: #333;">TBitSet</span> <span class="n" style="color: #333;">uniq</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="142" 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="LC142" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" 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="LC143" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</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="sc" style="color: #d14;">'C'</span><span class="p">)</span> <span class="n" style="color: #333;">uniq</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="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" 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="LC144" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="145" 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="LC145" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" 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="LC146" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Sum across fragments</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">meanisize</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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<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">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="149" 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="LC149" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="150" 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="LC150" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">halfwin</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="151" 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="LC151" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">halfwin</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

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<td class="diff-line-num new new_line" data-linenumber="152" 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="LC152" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="153" 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="LC153" class="line" lang="cpp">      <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfwin</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="cpp">      <span class="n" style="color: #333;">usum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">uniq</span><span class="p">[</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfwin</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" 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="LC155" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="cpp">    <span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">usum</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="158" 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="LC158" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="159" 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="LC159" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="160" 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">

160

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Bins on this chromosome</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="161" 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="LC161" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">binMap</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" 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">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="163" 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="LC163" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allbins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</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;">scanWindow</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" 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="LC164" class="line" lang="cpp">  <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">allbins</span><span class="p">,</span> <span class="n" style="color: #333;">ScanWindow</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="165" 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="LC165" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">allbins</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="166" 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="LC166" class="line" lang="cpp">    <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</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;">i</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;">scanWindow</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="167" 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="LC167" class="line" lang="cpp">    <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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 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;">scanWindow</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="168" 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="LC168" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="169" 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="LC169" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="170" 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="LC170" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Fill bin map</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="171" 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="LC171" class="line" lang="cpp">  <span class="n" style="color: #333;">binMap</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="n" style="color: #333;">LAST_BIN</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="172" 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="LC172" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">LAST_BIN</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: Too many scan windows on "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp">  <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="175" 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="LC175" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bin</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;">bin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">LAST_BIN</span><span class="p">));</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bin</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="n" style="color: #333;">binMap</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bin</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Mate map</span></span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">TMateMap</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">      <span class="n" style="color: #333;">TMateMap</span> <span class="n" style="color: #333;">mateMap</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Count reads</span></span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">      <span class="n" style="color: #333;">hts_itr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_itr_queryi</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="186" 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="LC186" class="line" lang="cpp">      <span class="n" style="color: #333;">bam1_t</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="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="187" 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="LC187" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">lastAlignedPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="188" 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="LC188" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="189" 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">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">sam_itr_next</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="p">,</span> <span class="n" style="color: #333;">rec</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 class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="190" 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">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">BAM_FSECONDARY</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FQCFAIL</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FDUP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FSUPPLEMENTARY</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">BAM_FUNMAP</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="191" 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">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FMUNMAP</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mtid</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" 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">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</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;">minQual</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="193" 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">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getSVType</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="194" 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">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfAlignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="196" 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">

196

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FPAIRED</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="197" 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="LC197" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Clean-up the read store for identical alignment positions</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="198" 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="LC198" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastAlignedPos</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="199" 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="LC199" class="line" lang="cpp">      <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp">      <span class="n" style="color: #333;">lastAlignedPos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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="cpp">    <span class="p">}</span></span>

</pre>

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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="cpp">  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="203" 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="LC203" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// First read</span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp">      <span class="n" style="color: #333;">lastAlignedPosReads</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)));</span></span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_pair</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp">      <span class="n" style="color: #333;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Second read</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp">      <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_pair_mate</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">mateMap</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">hv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">mateMap</span><span class="p">.</span><span class="n" style="color: #333;">end</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;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Mate discarded</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp">      <span class="n" style="color: #333;">mateMap</span><span class="p">[</span><span class="n" style="color: #333;">hv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Insert size filter</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">))</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">minNormalISize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">isize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">isize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">li</span><span class="p">.</span><span class="n" style="color: #333;">maxNormalISize</span><span class="p">))</span> <span class="n" style="color: #333;">midPoint</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">mpos</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">isize</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="LC219" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Count fragment</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">midPoint</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">midPoint</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_findScanWindow</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">],</span> <span class="n" style="color: #333;">binMap</span><span class="p">,</span> <span class="n" style="color: #333;">midPoint</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">cov</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">uniqContent</span><span class="p">[</span><span class="n" style="color: #333;">midPoint</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;">fragmentUnique</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;">meanisize</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">bin</span><span class="p">].</span><span class="n" style="color: #333;">uniqcov</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">totalCov</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">      <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">      <span class="n" style="color: #333;">hts_itr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="236" 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="LC236" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="237" 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="LC237" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="238" 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="LC238" class="line" lang="cpp">    </span>

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<td class="diff-line-num new new_line" data-linenumber="239" 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="LC239" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// clean-up</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">    <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">faiMap</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp">    <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp">    <span class="n" style="color: #333;">sam_close</span><span class="p">(</span><span class="n" style="color: #333;">samfile</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">></span></span>

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<td class="diff-line-num new new_line" data-linenumber="248" 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="LC248" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="249" 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="LC249" class="line" lang="cpp">  <span class="n" style="color: #333;">selectWindows</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ScanWindow</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="250" 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="LC250" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">noScanWindowSelection</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="251" 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="LC251" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Select all windows</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp">    <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="258" 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="LC258" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Pre-screen using PE layout, uniqueness and percent identity</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="259" 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="LC259" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Uniqueness</span></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">uniqratio</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="263" 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="LC263" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cov</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;">uniqratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">uniqcov</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cov</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="264" 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="LC264" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">uniqratio</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;">uniqueToTotalCovRatio</span><span class="p">)</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="265" 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="LC265" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="266" 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="LC266" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="267" 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="LC267" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Normalize user-defined scan windows to same length (10,000bp)</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasScanFile</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="271" 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="LC271" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="mi" style="color: #099;">10000</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</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="LC274" class="line" lang="cpp">      <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">uniqcov</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">      <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cov</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scale</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Get "normal" coverage windows of CN2</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TCountBounds</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp">      <span class="n" style="color: #333;">TCountBounds</span> <span class="n" style="color: #333;">cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">estCountBounds</span><span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp">      </span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Select CN2 windows</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cov</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cb</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cov</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cb</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">))</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">scanCounts</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">select</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="293" 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="LC293" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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<br>

</li>

<li id="76bf896cda9e6b76c0af8350e53bb4bc92d6d281">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#76bf896cda9e6b76c0af8350e53bb4bc92d6d281"><strong>src/tags.h</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,6 +11,10 @@ namespace torali {</td>

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#define DELLY_CHOP_REFSIZE 1000</span></span>

</pre>

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12

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<td class="diff-line-num new_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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_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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<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="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#ifndef DELLY_OUTOFBAND</span></span>

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<td class="diff-line-num new old_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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<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="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#define DELLY_OUTOFBAND -99999999</span></span>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp">  <span class="n" style="color: #333;">_translocation</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">DELLY_SVT_TRANS</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="145" 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="149" 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">@@ -145,8 +149,8 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">  <span class="n" style="color: #333;">_svSizeCheck</span><span class="p">(</span><span class="n" style="color: #333;">TSize</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">TSize</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Short reads</span></span>

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<td class="diff-line-num old old_line" data-linenumber="148" 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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<td class="diff-line-num new_line old" data-linenumber="152" 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="LC148" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svt</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 class="p">((</span> <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="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span>00</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" 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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<td class="diff-line-num new_line old" data-linenumber="152" 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="LC149" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span> <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="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span>00</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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="152" 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="LC152" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svt</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 class="p">((</span> <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="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span>00</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" 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="153" 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="LC153" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span> <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="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span>00</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span> <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="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">300</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">((</span> <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="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 old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="0295016a39c777dffa48c5e5efc6af0fb6982a0a">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#0295016a39c777dffa48c5e5efc6af0fb6982a0a"><strong>src/tegua.h</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="45" 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">@@ -45,6 +45,7 @@ namespace torali {</td>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">minRefSep</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maxReadSep</span><span class="p">;</span></span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">graphPruning</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="48" 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="LC48" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">minCliqueSize</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nchr</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">minimumFlankSize</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">indelExtension</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,7 +119,7 @@ namespace torali {</td>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp">     <span class="c1" style="color: #998; font-style: italic;">// SV Discovery</span></span>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp">     <span class="n" style="color: #333;">_clusterSRReads</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">validRegions</span><span class="p">,</span> <span class="n" style="color: #333;">svc</span><span class="p">,</span> <span class="n" style="color: #333;">tmpStore</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_line" data-linenumber="122" 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="LC122" class="line" lang="cpp">     </span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp">     <span class="c1" style="color: #998; font-style: italic;">// Assemble</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">

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">     <span class="n" style="color: #333;">assemble</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">validRegions</span><span class="p">,</span> <span class="n" style="color: #333;">svc</span><span class="p">,</span> <span class="n" style="color: #333;">tmpStore</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"></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">@@ -246,6 +247,7 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">   <span class="n" style="color: #333;">disc</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">     <span class="p">(</span><span class="s" style="color: #d14;">"mapqual,q"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint16_t</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;">minMapQual</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. mapping quality"</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">     <span class="p">(</span><span class="s" style="color: #d14;">"minclip,c"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">minClip</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">25</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. clipping length"</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="249" 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="250" 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="LC250" class="line" lang="cpp">     <span class="p">(</span><span class="s" style="color: #d14;">"min-clique-size,z"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">minCliqueSize</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. clique size"</span><span class="p">)</span>     </span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp">     <span class="p">(</span><span class="s" style="color: #d14;">"minrefsep,m"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">minRefSep</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">30</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. reference separation"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp">     <span class="p">(</span><span class="s" style="color: #d14;">"maxreadsep,n"</span><span class="p">,</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">program_options</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="kt" style="color: #458; font-weight: 600;">uint32_t</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;">maxReadSep</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">75</span><span class="p">),</span> <span class="s" style="color: #d14;">"max. read separation"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp">     <span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="296" 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">@@ -296,6 +298,9 @@ namespace torali {</td>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"dump"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasDumpFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasDumpFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"></span>

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<td class="diff-line-num new old_line" data-linenumber="299" 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="301" 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="LC301" class="line" lang="cpp">   <span class="c1" style="color: #998; font-style: italic;">// Clique size</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="299" 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="LC302" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minCliqueSize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minCliqueSize</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="LC303" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp">   <span class="c1" style="color: #998; font-style: italic;">// Check reference</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">is_regular_file</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file_size</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genome</span><span class="p">)))</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reference file is missing: "</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;">genome</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<br>

</li>

<li id="5f65ec0c183df81ed169516d4ec6c5508122dccd">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#5f65ec0c183df81ed169516d4ec6c5508122dccd"><strong>src/util.h</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,6 +16,10 @@</td>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">torali</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#ifndef LAST_BIN</span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#define LAST_BIN 65535</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp">  </span>

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">LibraryInfo</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">rs</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">median</span><span class="p">;</span></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="45" 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 +45,13 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp">  <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">  <span class="n" style="color: #333;">nContent</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</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;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">s</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="sc" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">s</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="sc" style="color: #d14;">'n'</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Decode Orientation</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span></span>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -199,7 +209,7 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sequenceLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp">    </span>

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<td class="diff-line-num new_line old" data-linenumber="212" 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="LC202" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">const</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_cigar</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">alen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</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="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">n_cigar</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -207,10 +217,17 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">alen</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">halfAlignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">halfAlignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">const</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</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="LC222" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">  <span class="n" style="color: #333;">lastAlignedPosition</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alignmentLength</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hash_lr</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">string_hash</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">qname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</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">@@ -293,6 +310,47 @@ namespace torali</td>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp">  <span class="n" style="color: #333;">setMinChrLen</span><span class="p">(</span><span class="n" style="color: #333;">bam_hdr_t</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">xx</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">minChrLen</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="316" 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="LC316" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chrlen</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</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="LC317" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">genomelen</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="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">

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refIndex</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;">refIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_targets</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">      <span class="n" style="color: #333;">chrlen</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp">      <span class="n" style="color: #333;">genomelen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_len</span><span class="p">[</span><span class="n" style="color: #333;">refIndex</span><span class="p">];</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">chrlen</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">chrlen</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">greater</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="323" 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="LC323" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">cumsum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="324" 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="LC324" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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 class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">chrlen</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="325" 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="LC325" class="line" lang="cpp">      <span class="n" style="color: #333;">cumsum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">chrlen</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="326" 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="LC326" class="line" lang="cpp">      <span class="n" style="color: #333;">minChrLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrlen</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="327" 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="LC327" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cumsum</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">genomelen</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xx</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="328" 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="LC328" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="296" 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="329" 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="LC329" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">minChrLen</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="296" 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="330" 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="LC330" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="296" 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="332" 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="LC332" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="296" 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="333" 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="LC333" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TConfig</span><span class="p">></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="334" 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="LC334" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="335" 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="LC335" class="line" lang="cpp">  <span class="n" style="color: #333;">chrNoData</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="n" style="color: #333;">hts_idx_t</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">idx</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check we have mapped reads on this chromosome</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">suffix</span><span class="p">(</span><span class="s" style="color: #d14;">"cram"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="338" 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="LC338" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">str</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">bamFile</span><span class="p">.</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="339" 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="LC339" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">suffix</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">suffix</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suffix</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">suffix</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 class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="340" 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="LC340" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">mapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="341" 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="LC341" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">unmapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="342" 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="LC342" class="line" lang="cpp">    <span class="n" style="color: #333;">hts_idx_get_stat</span><span class="p">(</span><span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mapped</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">unmapped</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="343" 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="LC343" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mapped</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="344" 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="LC344" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="296" 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="345" 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="LC345" class="line" lang="cpp">  <span class="p">}</span>    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="346" 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="LC346" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="347" 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="LC347" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hash_se</span><span class="p">(</span><span class="n" style="color: #333;">bam1_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="348" 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="LC348" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="349" 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="LC349" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hash_combine</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="350" 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="LC350" class="line" lang="cpp">    <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hash_combine</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="351" 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="LC351" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seed</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="296" 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="352" 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="LC352" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="353" 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="LC353" class="line" lang="cpp">  </span>

</pre>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>

</pre>

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355

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp">  <span class="n" style="color: #333;">getSMTag</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sampleName</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="298" 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">

298

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<td class="diff-line-num new_line" data-linenumber="356" 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">

356

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">smIdentifiers</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="564" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -564,8 +622,8 @@ namespace torali</td>

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<td class="diff-line-num old_line" data-linenumber="564" 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">

564

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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="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="565" 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">

565

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<td class="diff-line-num new_line" data-linenumber="623" 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">

623

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="566" 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">

566

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<td class="diff-line-num new_line" data-linenumber="624" 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">

624

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">mad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mad</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="567" 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">

567

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<td class="diff-line-num new_line old" data-linenumber="625" 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="LC567" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">maxNormalISize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">5</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="568" 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">

568

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<td class="diff-line-num new_line old" data-linenumber="625" 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="LC568" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">minNormalISize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">5</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="569" 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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">maxNormalISize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">madNormalCutoff</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="569" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="626" 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">

626

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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">minNormalISize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">c</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">madNormalCutoff</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="569" 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">

569

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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="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">minNormalISize</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;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">minNormalISize</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="570" 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">

570

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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">maxISizeCutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</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;">madCutoff</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="571" 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">

571

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<td class="diff-line-num new_line" data-linenumber="629" 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">

629

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp">      <span class="n" style="color: #333;">sampleLib</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">minISizeCutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">median</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;">madCutoff</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mad</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="f92b0b9f2ecd99eca4c19d9518afaae33bc2d58a">

<a href="https://salsa.debian.org/med-team/delly/-/commit/77fba0a1f8ba40e9e450e816f55ca45ca3013089#f92b0b9f2ecd99eca4c19d9518afaae33bc2d58a"><strong>src/version.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,7 +5,7 @@ namespace torali</td>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" 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">

7

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<td class="diff-line-num new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

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<td class="diff-line-num new_line old" data-linenumber="8" 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="LC8" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">dellyVersionNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.8.<span class="idiff left right">3</span>"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">dellyVersionNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.8.<span class="idiff left right">5</span>"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line" data-linenumber="9" 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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_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">

10

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<td class="diff-line-num 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp">  <span class="kr" style="font-weight: 600;">inline</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line" data-linenumber="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">printTitle</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">title</span><span class="p">)</span> </span>

</pre>

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