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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/faeb27c17a5e3c2645c14c6778f2897982887c26">faeb27c1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-17T15:27:31+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.7</pre>
</li>
</ul>
<h4>21 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6a7d105cee155e00142e5ced05fbd9aa83f45b8b">
.github/workflows/docker.yml
</a>
</li>
<li class="file-stats">
<a href="#b2a53ffd0c4c3d50e7f9adca1be4eb48c3e0f141">
<span class="new-file">
+
R/cnv.R
</span>
</a>
</li>
<li class="file-stats">
<a href="#5f978958190b293037054bd9d5e795d0b92d1ca8">
R/rd.R
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9dc82939741eb76d609db1ac16b1398c80eb0e27">
src/assemble.h
</a>
</li>
<li class="file-stats">
<a href="#5d54834e56c96241edb77b58abde4276dd9e90ef">
src/bolog.h
</a>
</li>
<li class="file-stats">
<a href="#59f95844690da404b62e84bbca3c42599ea89b7a">
<span class="new-file">
+
src/classify.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#6a965fc172da372b399f988708853bec938e4290">
src/cnv.h
</a>
</li>
<li class="file-stats">
<a href="#dcad3ddfd75218047069bbaa2acab307a0655169">
src/coral.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
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</li>
<li class="file-stats">
<a href="#836bf99511b7d355c156c4bd68f24fd0b7ce69c9">
src/genotype.h
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</li>
<li class="file-stats">
<a href="#32e45cc4e811e711ac7f53e87e90add0070af5a7">
src/junction.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="#8f130c1406eeae226d6453bcf3ab844ecd2c707b">
src/msa.h
</a>
</li>
<li class="file-stats">
<a href="#de10b670208808941807d0db7069159f2749af37">
src/split.h
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</li>
<li class="file-stats">
<a href="#76bf896cda9e6b76c0af8350e53bb4bc92d6d281">
src/tags.h
</a>
</li>
<li class="file-stats">
<a href="#0295016a39c777dffa48c5e5efc6af0fb6982a0a">
src/tegua.h
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</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="6a7d105cee155e00142e5ced05fbd9aa83f45b8b">
<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#6a7d105cee155e00142e5ced05fbd9aa83f45b8b"><strong>.github/workflows/docker.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">@@ -2,19 +2,24 @@ name: Docker CI</td>
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5" 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="5" 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="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 class="diff-line-num old old_line" data-linenumber="6" 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="5" 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="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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="5" 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="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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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="s" style="color: #d14;">master</span></span>
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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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"></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">
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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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<td class="diff-line-num 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="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="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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="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="LC11" class="line" lang="yaml"></span>
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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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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">main</span><span class="pi">:</span></span>
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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="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="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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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="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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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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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<td class="diff-line-num new_line old" data-linenumber="11" 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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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="11" 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="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>
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<td class="diff-line-num old old_line" data-linenumber="16" 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="11" 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="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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="11" 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="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">username</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.DOCKER_USERNAME }}</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.DOCKER_PASSWORD }}</span></span>
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19
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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>
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20
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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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<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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up QEMU</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker/setup-qemu-action@v1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Docker Buildx</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker/setup-buildx-action@v1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Login to DockerHub</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker/login-action@v1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">username</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.DOCKER_USERNAME }}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.DOCKER_PASSWORD }}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build and push</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker_build</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker/build-push-action@v2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="s" style="color: #d14;">dellytools/delly:latest</span></span></pre>
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<li id="b2a53ffd0c4c3d50e7f9adca1be4eb48c3e0f141">
<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#b2a53ffd0c4c3d50e7f9adca1be4eb48c3e0f141"><strong>R/cnv.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">
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>
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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;">reshape2</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="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>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="r"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" 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>
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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="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;">F</span><span class="p">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="r"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="r"><span class="n" style="color: #333;">colnames</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 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;">"cnv"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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="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="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;">"cnv"</span><span class="p">))</span></span>
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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="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cn</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">round</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="r"><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;">$</span><span class="n" style="color: #333;">cn</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">></span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">9</span><span class="p">,]</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cn</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;">9</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cn</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">factor</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cn</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="m" style="color: #099;">0</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">9</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="r"><span class="n" style="color: #333;">nsamples</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;">length</span><span class="p">(</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;">variable</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="r"><span class="n" style="color: #333;">nbins</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;">sqrt</span><span class="p">(</span><span class="n" style="color: #333;">nsamples</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" 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="n" style="color: #333;">nbins</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;">30</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;">nbins</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;">30</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="LC16" class="line" lang="r"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># Plot CNVs</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="r"><span class="k" style="font-weight: 600;">for</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">CNV</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;">cnv</span><span class="p">))</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" 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;">CNV</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><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;">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;">cnv</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;">CNV</span><span class="p">,]</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="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;">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;">value</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</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="m" style="color: #099;">0</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">9</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="LC23" 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_histogram</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;">subset</span><span class="p">(</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;">cn</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;">i</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;">fill</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cn</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">bins</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nbins</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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;">xlab</span><span class="p">(</span><span class="s2" style="color: #d14;">"Copy-number"</span><span class="p">)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" 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;">"Count"</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" 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;">breaks</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">0</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">10</span><span class="p">,</span><span class="w" style="color: #bbb;"> </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>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># p = p + scale_fill_manual(values=c("#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a"), drop=F)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" 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_fill_manual</span><span class="p">(</span><span class="n" style="color: #333;">values</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;">"#ff7f00"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"#1f78b4"</span><span class="p">,</span><span class="s2" style="color: #d14;">"#33a02c"</span><span class="p">,</span><span class="s2" style="color: #d14;">"#e31a1c"</span><span class="p">,</span><span class="s2" style="color: #d14;">"#6a3d9a"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"#fdbf6f"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"#a6cee3"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"#b2df8a"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"#fb9a99"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"#cab2d6"</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">drop</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">F</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" 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;">ggtitle</span><span class="p">(</span><span class="n" style="color: #333;">CNV</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" 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="n" style="color: #333;">CNV</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>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="r"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#5f978958190b293037054bd9d5e795d0b92d1ca8"><strong>R/rd.R</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">@@ -9,18 +9,28 @@ chrNamesShort = c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","</td>
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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>
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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>
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11
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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>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="r"><span class="n" style="color: #333;">seg</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;">data.frame</span><span class="p">()</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" 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;">length</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="m" style="color: #099;">1</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">seg</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;">2</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;">F</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"\t"</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">colnames</span><span class="p">(</span><span class="n" style="color: #333;">seg</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;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"chr"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"start"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"end"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"id"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"cn"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="r"><span class="p">}</span></span>
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12
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="r"></span>
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13
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># Fix chromosome ordering</span></span>
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14
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="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;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%in%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrNamesShort</span><span class="p">))</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrNamesLong</span><span class="p">;</span><span class="w" style="color: #bbb;"> </span><span class="p">}</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrNamesShort</span><span class="p">;</span><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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15
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="r"><span class="n" style="color: #333;">x</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">$</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>
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16
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<pre style="margin: 0;"> <span id="LC21" 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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<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="r"><span class="k" style="font-weight: 600;">if</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;">seg</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="m" style="color: #099;">0</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">seg</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;">seg</span><span class="p">[</span><span class="n" style="color: #333;">seg</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%in%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrs</span><span class="p">,]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">seg</span><span class="o" style="font-weight: 600;">$</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;">seg</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="LC25" class="line" lang="r"><span class="p">}</span></span>
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17
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="r"></span>
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18
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;"># Whole genome</span></span>
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19
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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC28" 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>
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<pre style="margin: 0;">+<span id="LC29" 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;"><span class="idiff left">color</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"black"</span></span><span class="p"><span class="idiff">,</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff">fill</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"black"</span></span><span class="p"><span class="idiff">,</span></span><span class="w" style="color: #bbb;"><span class="idiff right"> </span></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>
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21
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30
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<pre style="margin: 0;"> <span id="LC30" 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>
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22
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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
31
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<pre style="margin: 0;"> <span id="LC31" 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>
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23
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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
32
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<pre style="margin: 0;"> <span id="LC32" 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>
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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">
33
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<pre style="margin: 0;">+<span id="LC33" 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="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">seg</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;">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_segment</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;">seg</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;">cn</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xend</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">yend</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cn</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;">"#31a354"</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;">1.2</span><span class="p">);</span><span class="w" style="color: #bbb;"> </span><span class="p">}</span></span>
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24
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34
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<pre style="margin: 0;"> <span id="LC34" 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>
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25
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35
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<pre style="margin: 0;"> <span id="LC35" 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>
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26
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<td class="diff-line-num 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">
36
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<pre style="margin: 0;"> <span id="LC36" 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>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,10 +41,12 @@ print(warnings())</td>
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31
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41
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<pre style="margin: 0;"> <span id="LC41" 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>
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32
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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
42
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<pre style="margin: 0;"> <span id="LC42" 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>
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33
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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">
43
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<pre style="margin: 0;"> <span id="LC43" 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;">$</span><span class="n" style="color: #333;">chr</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">==</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">chrname</span><span class="p">,]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sl</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">seg</span><span class="p">[</span><span class="n" style="color: #333;">seg</span><span class="o" style="font-weight: 600;">$</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>
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<pre style="margin: 0;"> <span id="LC45" 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>
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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>
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<pre style="margin: 0;">+<span id="LC46" 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;"><span class="idiff left">color</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"black"</span></span><span class="p"><span class="idiff">,</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff">fill</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"black"</span></span><span class="p"><span class="idiff">,</span></span><span class="w" style="color: #bbb;"><span class="idiff right"> </span></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>
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<pre style="margin: 0;"> <span id="LC47" 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>
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<pre style="margin: 0;"> <span id="LC48" 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>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">if</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;">sl</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;">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_segment</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;">sl</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;">cn</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xend</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">yend</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cn</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;">"#31a354"</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;">1.2</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="LC50" 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>
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<pre style="margin: 0;"> <span id="LC51" 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>
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<pre style="margin: 0;"> <span id="LC52" 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>
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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>
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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>
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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 <span class="idiff left">visualized using </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Delly-maze</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/dellytools/maze</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> and</span> <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>
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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 <span class="idiff left">annotated using </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Delly-sansa</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/dellytools/sansa</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> and visualized using </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Delly-maze</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/dellytools/maze</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> or</span> <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>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gh" style="color: #999;">Installing Delly</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">@@ -54,16 +54,6 @@ 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>
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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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<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>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"></span>
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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>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"></span>
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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>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"></span>
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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>
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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="LC57" class="line" lang="markdown"><span class="gh" style="color: #999;">Somatic SV calling</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,6 +101,16 @@ Germline SV calling</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly filter -f germline -o germline.bcf merged.bcf`</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="gh" style="color: #999;">Delly for long reads from PacBio or ONT</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------------------------</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown">Delly also has a long-read (lr) SV discovery mode.</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly lr -y ont -g hg19.fa -x hg19.excl input.bam`</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly lr -y pb -g hg19.fa -x hg19.excl input.bam`</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"></span>
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114
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114
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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>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,21 +118,86 @@ You can generate read-depth profiles with delly. This requires a mappability map</td>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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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>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"></span>
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121
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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>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown">The command to count reads in 10kbp <span class="idiff left right">mappable </span>windows and normalize the coverage is:</span>
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122
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly <span class="idiff left right">rd</span> -a -g hg19.fa -m hg19.map input.bam`</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly <span class="idiff left right">cnv</span> -a -g hg19.fa -m hg19.map input.bam`</span></span>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="markdown">The output file <span class="idiff left right">can be plotted using R</span> to generate normalized copy-number profiles:</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown">The output file <span class="sb" style="color: #d14;"><span class="idiff left">`out.cov.gz`</span></span><span class="idiff"> can be plotted using </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">R</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://www.r-project.org/</span></span><span class="p"><span class="idiff right">)</span></span> to generate normalized copy-number profiles:</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"></span>
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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>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"></span>
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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>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown"></span>
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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>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="gh" style="color: #999;">Copy-number segmentation</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown">Read-depth profiles can also be segmented at the same time.</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly cnv -a -u -g hg19.fa -m hg19.map input.bam`</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown">The segmentation is in VCF format but you can extract a BED-like file using bcftools.</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bcftools query -f "%CHROM\t%POS\t%INFO/END\t%ID\t[%RDCN]\n" cnv.bcf > segmentation.bed`</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown">Plotting:</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"><span class="sb" style="color: #d14;">`Rscript R/rd.R out.cov.gz segmentation.bed`</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"><span class="gh" style="color: #999;">Germline CNV calling</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown">Delly uses GC and mappability fragment correction to call CNVs. This requires a <span class="p">[</span><span class="nv" style="color: #008080;">mappability map</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gear.embl.de/data/delly/</span><span class="p">)</span>.</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"><span class="p">*</span> Call CNVs for each sample and optionally refine breakpoints using delly SV calls</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"></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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly cnv -o c1.bcf -g hg19.fa -m hg19.map -l delly.sv.bcf input.bam`</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"><span class="p">*</span> Merge CNVs into a unified site list</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly merge -e -p -o sites.bcf -m 1000 -n 100000 c1.bcf c2.bcf ... cN.bcf`</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"><span class="p">*</span> Genotype CNVs for each sample</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"></span>
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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="markdown"><span class="sb" style="color: #d14;">`delly cnv -u -v sites.bcf -g hg19.fa -m hg19.map -o geno1.bcf input.bam`</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"><span class="p">*</span> Merge genotypes using <span class="p">[</span><span class="nv" style="color: #008080;">bcftools</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/samtools/bcftools</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bcftools merge -m id -O b -o merged.bcf geno1.bcf ... genoN.bcf`</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="p">*</span> Filter for germline CNVs</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"></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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly classify -f germline -o filtered.bcf merged.bcf`</span></span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"></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="markdown"><span class="p">*</span> Optional: Plot copy-number distribution for large number of samples (>>100)</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"></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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bcftools query -f "%ID[\t%RDCN]\n" filtered.bcf > plot.tsv`</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"><span class="sb" style="color: #d14;">`Rscript R/cnv.R plot.tsv`</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"><span class="gh" style="color: #999;">Somatic copy-number alterations (SCNAs)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------------------------</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="markdown"><span class="p">*</span> For somatic copy-number alterations, delly first segments the tumor genome (<span class="sb" style="color: #d14;">`-u`</span> is required). Depending on the coverage, tumor purity and heterogeneity you can adapt parameters <span class="sb" style="color: #d14;">`-z`</span>, <span class="sb" style="color: #d14;">`-t`</span> and <span class="sb" style="color: #d14;">`-x`</span> which control the sensitivity of SCNA detection.</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="markdown"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly cnv -u -z 10000 -o tumor.bcf -c tumor.cov.gz -g hg19.fa -m hg19.map tumor.bam`</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"><span class="p">*</span> Then these tumor SCNAs are genotyped in the control sample (<span class="sb" style="color: #d14;">`-u`</span> is required).</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly cnv -u -v tumor.bcf -o control.bcf -g hg19.fa -m hg19.map control.bam`</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"><span class="p">*</span> The VCF IDs are matched between tumor and control. Thus, you can merge both files using <span class="p">[</span><span class="nv" style="color: #008080;">bcftools</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/samtools/bcftools</span><span class="p">)</span>.</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bcftools merge -m id -O b -o tumor_control.bcf tumor.bcf control.bcf`</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"><span class="p">*</span> Somatic filtering requires a tab-delimited sample description file where the first column is the sample id (as in the VCF/BCF file) and the second column is either tumor or control.</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="markdown"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="markdown"><span class="sb" style="color: #d14;">`delly classify -p -f somatic -o somatic.bcf -s samples.tsv tumor_control.bcf`</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"><span class="p">*</span> Optional: Plot the SCNAs using bcftools and R.</span>
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132
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="markdown"><span class="sb" style="color: #d14;">`<span class="idiff left right">zgrep "^GC" stats.gz > gc.table</span>`</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown"><span class="sb" style="color: #d14;">`<span class="idiff left right">bcftools query -s tumor -f "%CHROM\t%POS\t%INFO/END\t%ID\t[%RDCN]\n" somatic.bcf > segmentation.bed</span>`</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="markdown"><span class="sb" style="color: #d14;">`Rscript R/<span class="idiff left right">gcbias.R gc.table</span>`</span></span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"><span class="sb" style="color: #d14;">`Rscript R/<span class="idiff left right">rd.R tumor.cov.gz segmentation.bed</span>`</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="markdown"><span class="gh" style="color: #999;">FAQ</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="206" style="width: 35px; color: rgba(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">@@ -141,10 +206,10 @@ FAQ</td>
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<pre style="margin: 0;"> <span id="LC206" 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>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="markdown"><span class="p">*</span> Can Delly be used on a non-diploid genome? </span>
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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>
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<pre style="margin: 0;">+<span id="LC209" 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 class="idiff left right"> The CNV calling allows to set the baseline ploidy on the command-line.</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="markdown"><span class="p">*</span> Delly is running too slowly what can I do? </span>
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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>
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<pre style="margin: 0;">+<span id="LC212" 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"> Lastly, </span><span class="sb" style="color: #d14;"><span class="idiff">`-z`</span></span><span class="idiff right"> can be set to 5 for high-coverage data.</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="markdown"><span class="p">*</span> Are non-unique alignments, multi-mappings and/or multiple split-read alignments allowed? </span>
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<pre style="margin: 0;"> <span id="LC215" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="158" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -158,7 +223,7 @@ There is a delly discussion group [delly-users](http://groups.google.com/d/forum</td>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="markdown"><span class="p">*</span> Docker/Singularity support? </span>
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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(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="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> and singularity containers (<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>.sif files) are part of the <span class="p">[</span><span class="nv" style="color: #008080;">delly release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/dellytools/delly/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="markdown"><span class="p">*</span> Bioconda support? </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"><span class="p">*</span> Bioconda support? <span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC227" 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>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#9dc82939741eb76d609db1ac16b1398c80eb0e27"><strong>src/assemble.h</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">@@ -17,6 +17,7 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">inslen</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Only required for junction count map</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">SeqSlice</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">svid</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">sstart</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">inslen</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">qual</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="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">SeqSlice</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;">sv</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;">sst</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;">il</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">svid</span><span class="p">(</span><span class="n" style="color: #333;">sv</span><span class="p">),</span> <span class="n" style="color: #333;">sstart</span><span class="p">(</span><span class="n" style="color: #333;">sst</span><span class="p">),</span> <span class="n" style="color: #333;">inslen</span><span class="p">(</span><span class="n" style="color: #333;">il</span><span class="p">),</span> <span class="n" style="color: #333;">qual</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC23" 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">@@ -31,7 +32,6 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SV consensus done</span></span>
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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;">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;">svcons</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">.</span><span class="n" style="color: #333;">size</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="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">maxReadPerSV</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open file handles</span></span>
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<pre style="margin: 0;"> <span id="LC37" 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;">samFile</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">TSamFile</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">@@ -76,7 +76,7 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << svs[svid].svStart << ',' << svs[svid].svEnd << ',' << svs[svid].svt << ',' << svid << " SV" << std::endl;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << seed << '\t' << srStore[seed][ri].svid << '\t' << srStore[seed][ri].sstart << '\t' << srStore[seed][ri].inslen << '\t' << sv[srStore[seed][ri].svid].srSupport << '\t' << sv[srStore[seed][ri].svid].svt << std::endl;</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"></span>
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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 class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">svcons</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 right">]</span>)</span> <span class="p">{</span></span>
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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 class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">svcons</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="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seqStore</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">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="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">maxReadPerSV</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get sequence</span></span>
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<pre style="margin: 0;"> <span id="LC81" 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="LC82" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,18 +95,23 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sPos</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;">sPos</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="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ePos</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;">readlen</span><span class="p">)</span> <span class="n" style="color: #333;">ePos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readlen</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Min. seq length and max insertion size, 10kbp?</span></span>
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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;">ePos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sPos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">window</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">ePos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sPos</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;"><span class="idiff left right">10000</span></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="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">ePos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sPos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">window</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">ePos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sPos</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p"><span class="idiff left">(</span></span><span class="mi" style="color: #099;"><span class="idiff">10000</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">window</span></span><span class="p"><span class="idiff right">)</span>))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC99" 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;">seqalign</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">sPos</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">ePos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sPos</span><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;">if</span> <span class="p">((</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">6</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">refIndex</span><span class="p">)</span> <span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">seqalign</span><span class="p">);</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="p">}</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">seqalign</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"></span>
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102
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Enough split-reads?</span></span>
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103
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106
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<pre style="margin: 0;"> <span id="LC106" 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;">_translocation</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">refIndex</span><span class="p">))</span> <span class="p">{</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">maxReadPerSV</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;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">srSupport</span><span class="p">))</span> <span class="p">{</span></span>
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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;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;"><span class="idiff left">c</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">maxReadPerSV</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;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">srSupport</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">msaSuccess</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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106
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</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="p">{</span></span>
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107
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << svs[svid].svStart << ',' << svs[svid].svEnd << ',' << svs[svid].svt << ',' << svid << " SV" << std::endl;</span></span>
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108
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(typename TSequences::iterator it = seqStore[svid].begin(); it != seqStore[svid].end(); ++it) std::cerr << *it << std::endl;</span></span>
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109
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">msa</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">],</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">consensus</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//outputConsensus(hdr, svs[svid], svs[svid].consensus);</span></span>
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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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">5</span><span class="p">))</span> <span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">consensus</span><span class="p">);</span></span>
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110
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << svs[svid].consensus << std::endl;</span></span>
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111
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignConsensus</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="n" style="color: #333;">seq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">]))</span> <span class="n" style="color: #333;">msaSuccess</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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112
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << msaSuccess << std::endl;</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">@@ -128,14 +133,30 @@ namespace torali</td>
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128
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133
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<pre style="margin: 0;"> <span id="LC133" 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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129
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134
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<pre style="margin: 0;"> <span id="LC134" 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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130
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="p">}</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Handle left-overs</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" 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;">svid</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;">svid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">svcons</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;">svid</span><span class="p">)</span> <span class="p">{</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="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;">svcons</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">])</span> <span class="p">{</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" 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;">_translocation</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">refIndex</span><span class="p">))</span> <span class="p">{</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Handle left-overs and translocations</span></span>
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137
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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;">int32_t</span> <span class="n" style="color: #333;">refIndex2</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;">refIndex2</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="n" style="color: #333;">refIndex2</span><span class="p">)</span> <span class="p">{</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" 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;">sndSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" 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;">svid</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;">svid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">svcons</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;">svid</span><span class="p">)</span> <span class="p">{</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" 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;">svcons</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">])</span> <span class="p">{</span></span>
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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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">refIndex</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">refIndex2</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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135
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">msaSuccess</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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136
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143
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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;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</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="p">{</span></span>
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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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Lazy loading of references</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">
145
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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;">refIndex</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">refIndex2</span><span class="p">)</span> <span class="p">{</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sndSeq</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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<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;">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>
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148
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<pre style="margin: 0;">+<span id="LC148" 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;">refIndex2</span><span class="p">]);</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">sndSeq</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;">fai</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;">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;">refIndex2</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="p">}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << svs[svid].svStart << ',' << svs[svid].svEnd << ',' << svs[svid].svt << ',' << svid << " SV" << std::endl;</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(typename TSequences::iterator it = seqStore[svid].begin(); it != seqStore[svid].end(); ++it) std::cerr << *it << std::endl;</span></span>
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137
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">msa</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">seqStore</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">],</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">consensus</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignConsensus</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="n" style="color: #333;">seq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">]))</span> <span class="n" style="color: #333;">msaSuccess</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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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//outputConsensus(hdr, svs[svid], svs[svid].consensus);</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">5</span><span class="p">))</span> <span class="n" style="color: #333;">reverseComplement</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">consensus</span><span class="p">);</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "Consensus: " << svs[svid].consensus << std::endl;</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignConsensus</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="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">sndSeq</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">]))</span> <span class="n" style="color: #333;">msaSuccess</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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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << msaSuccess << std::endl;</span></span>
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139
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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161
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<pre style="margin: 0;"> <span id="LC161" 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;">msaSuccess</span><span class="p">)</span> <span class="p">{</span></span>
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141
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">consensus</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</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">@@ -146,6 +167,7 @@ namespace torali</td>
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146
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">svcons</span><span class="p">[</span><span class="n" style="color: #333;">svid</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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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="p">}</span></span>
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148
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="p">}</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sndSeq</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;">sndSeq</span><span class="p">);</span></span>
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149
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="p">}</span></span>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> </span>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#5d54834e56c96241edb77b58abde4276dd9e90ef"><strong>src/bolog.h</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">@@ -2,6 +2,7 @@</td>
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2
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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 BOLOG_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/math/special_functions/round.hpp></span></span>
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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/math/distributions/normal.hpp></span></span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><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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7
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8
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<pre style="margin: 0;"> <span id="LC8" 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">@@ -82,7 +83,60 @@ struct BoLog {</td>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">gls</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">+</span> <span 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="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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83
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">gls</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</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;">float</span><span class="p">)</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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84
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"></span>
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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="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="LC89" 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="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">_computeCNLs</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;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mean</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;">sd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gl</span><span class="p">,</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;">gqval</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;">file_c</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="c1" style="color: #998; font-style: italic;">// Compute copy-number likelihoods</span></span>
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<pre style="margin: 0;">+<span id="LC92" 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;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">normal</span> <span class="n" style="color: #333;">s</span><span class="p">(</span><span class="n" style="color: #333;">mean</span><span class="p">,</span> <span class="n" style="color: #333;">sd</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;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">geno</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;">geno</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_CN</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">geno</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prob</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;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">geno</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</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;">log10</span><span class="p">(</span><span class="n" style="color: #333;">prob</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">SMALLEST_GL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">SMALLEST_GL</span><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>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">glBest</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</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="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">glBest2nd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</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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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">glBest</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">glBest2nd</span><span class="p">])</span> <span class="p">{</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">glBest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</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="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">glBest2nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</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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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="p">}</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" 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;">geno</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;">geno</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_CN</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">geno</span><span class="p">)</span> <span class="p">{</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">glBest2nd</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">glBest</span><span class="p">])</span> <span class="p">{</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">glBest2nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glBest</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">glBest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">;</span></span>
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109
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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>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">glBest2nd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="p">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="p">}</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="p">}</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> </span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Variant quality</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">glObs</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;">log10</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;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">mean</span><span class="p">));</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">glObs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">glObs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">SMALLEST_GL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">glObs</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">SMALLEST_GL</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">plVariant</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;">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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">glObs</span><span class="p">);</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">plPloidy</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;">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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_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="p">]);</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">varqual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plPloidy</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">plVariant</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// GQ</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">plBest</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;">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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">glBest</span><span class="p">]);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">plBest2nd</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;">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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">glBest2nd</span><span class="p">]);</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <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="n" style="color: #333;">plBest2nd</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">plBest</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> </span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Rescale by best genotype</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">glBestVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">glBest</span><span class="p">];</span></span>
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129
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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;">geno</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;">geno</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">MAX_CN</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">geno</span><span class="p">)</span> <span class="n" style="color: #333;">gl</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">geno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">glBestVal</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Variant quality</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">varqual</span><span class="p">;</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" 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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136
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<pre style="margin: 0;">+<span id="LC136" 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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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">_computeCNLs</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;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mean</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;">sd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gl</span><span class="p">,</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;">gqval</span><span class="p">)</span> <span class="p">{</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_computeCNLs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">mean</span><span class="p">,</span> <span class="n" style="color: #333;">sd</span><span class="p">,</span> <span class="n" style="color: #333;">gl</span><span class="p">,</span> <span class="n" style="color: #333;">gqval</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"><span class="p">}</span></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef CLASSIFY_H</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define CLASSIFY_H</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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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 <iostream></span></span>
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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 <fstream></span></span>
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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/unordered_map.hpp></span></span>
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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/graph/adjacency_list.hpp></span></span>
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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/graph/connected_components.hpp></span></span>
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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/program_options/cmdline.hpp></span></span>
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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/program_options/options_description.hpp></span></span>
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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;">#include <boost/program_options/parsers.hpp></span></span>
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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/program_options/variables_map.hpp></span></span>
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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/date_time/posix_time/posix_time.hpp></span></span>
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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/date_time/gregorian/gregorian.hpp></span></span>
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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/stream.hpp></span></span>
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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/stream_buffer.hpp></span></span>
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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>
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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/filtering_stream.hpp></span></span>
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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 <boost/iostreams/filter/zlib.hpp></span></span>
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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 <boost/iostreams/filter/gzip.hpp></span></span>
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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 <boost/icl/interval_map.hpp></span></span>
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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 <boost/filesystem.hpp></span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/tokenizer.hpp></span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/progress.hpp></span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/accumulators/accumulators.hpp></span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <boost/accumulators/statistics.hpp></span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/sam.h></span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/vcf.h></span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/tbx.h></span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/types.h></span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/stat.h></span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unistd.h></span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <zlib.h></span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tags.h"</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "version.h"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util.h"</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "modvcf.h"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"></span>
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44
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<pre style="margin: 0;">+<span id="LC44" 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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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="p">{</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">ClassifyConfig</span> <span class="p">{</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">filterForPass</span><span class="p">;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasSampleFile</span><span class="p">;</span></span>
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51
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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;">minsize</span><span class="p">;</span></span>
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52
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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;">maxsize</span><span class="p">;</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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54
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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;">ploidy</span><span class="p">;</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pgerm</span><span class="p">;</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">maxsd</span><span class="p">;</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cn_offset</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" 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;">filter</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" 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;">tumorSet</span><span class="p">;</span></span>
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60
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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;">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;">controlSet</span><span class="p">;</span></span>
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61
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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;">outfile</span><span class="p">;</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" 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;">samplefile</span><span class="p">;</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" 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;">vcffile</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>
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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;">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;">TClassifyConfig</span><span class="p">></span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="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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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="n" style="color: #333;">classifyRun</span><span class="p">(</span><span class="n" style="color: #333;">TClassifyConfig</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="p">{</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Load bcf file</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ifile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">vcffile</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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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open output VCF file</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ofile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</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;">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;">"wb"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hdr_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_dup</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="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;">filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"somatic"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_remove</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HL_INFO</span><span class="p">,</span> <span class="s" style="color: #d14;">"SOMATIC"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Somatic copy-number variant.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_remove</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HL_INFO</span><span class="p">,</span> <span class="s" style="color: #d14;">"PGERM"</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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=PGERM,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Probability of being germline.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_remove</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HL_INFO</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNDIFF"</span><span class="p">);</span></span>
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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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=CNDIFF,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Absolute tumor-normal CN difference.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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">
85
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<pre style="margin: 0;">+<span id="LC85" 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="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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_remove</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HL_INFO</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNSHIFT"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=CNSHIFT,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Estimated CN shift.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_remove</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HL_INFO</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNSD"</span><span class="p">);</span></span>
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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="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=CNSD,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Estimated CN standard deviation.</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="p">}</span></span>
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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">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_hdr_write</span><span class="p">(</span><span class="n" style="color: #333;">ofile</span><span class="p">,</span> <span class="n" style="color: #333;">hdr_out</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;">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;">"Error: Failed to write BCF header!"</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="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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// VCF fields</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nsvend</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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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <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;">svend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nsvt</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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97
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<pre style="margin: 0;">+<span id="LC97" 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;">svt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngqval</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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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <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;">gqval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncnval</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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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <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;">cnval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ncnl</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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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nrdcn</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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rdcn</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nrdsd</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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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rdsd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">germline</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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109
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<pre style="margin: 0;">+<span id="LC109" 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;">filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"germline"</span><span class="p">)</span> <span class="n" style="color: #333;">germline</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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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse BCF</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" 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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<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="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;">"Filtering 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>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf1_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;">bcf_init1</span><span class="p">();</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</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="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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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_unpack</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_UN_INFO</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check SV type</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_get_info_string</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;">"SVTYPE"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">svt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nsvt</span><span class="p">);</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" 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;">"CNV"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check PASS</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">pass</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="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">
124
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<pre style="margin: 0;">+<span id="LC124" 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;">filterForPass</span><span class="p">)</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_has_filter</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="k" style="font-weight: 600;">const_cast</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="p">(</span><span class="s" style="color: #d14;">"PASS"</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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125
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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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pass</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check size</span></span>
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<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">
128
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<pre style="margin: 0;">+<span id="LC128" 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="n" style="color: #333;">rec</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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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <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;">"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>
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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">
130
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<pre style="margin: 0;">+<span id="LC130" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">svend</span><span class="p">;</span></span>
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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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">svEnd</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">svlen</span> <span class="o" style="font-weight: 600;">=</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="p">;</span></span>
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133
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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;">svlen</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;">svlen</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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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check copy-number</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_unpack</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_UN_ALL</span><span class="p">);</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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_get_format_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;">"GQ"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gqval</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ngqval</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_get_format_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;">"CN"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cnval</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ncnval</span><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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_get_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;">"CNL"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cnl</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ncnl</span><span class="p">);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_get_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;">"RDCN"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rdcn</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nrdcn</span><span class="p">);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_get_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;">"RDSD"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rdsd</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nrdsd</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"></span>
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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="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;">float</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TCnSd</span><span class="p">;</span></span>
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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">
144
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<pre style="margin: 0;">+<span id="LC144" 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;">TCnSd</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSampleDist</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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">TSampleDist</span> <span class="n" style="color: #333;">control</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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">TSampleDist</span> <span class="n" style="color: #333;">tumor</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">
147
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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;">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;">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="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="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">germline</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;">controlSet</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">samples</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;">controlSet</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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<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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Control or population genomics</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">control</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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">rdcn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">rdsd</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">germline</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;">tumorSet</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">samples</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;">tumorSet</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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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Tumor</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">tumor</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;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">rdcn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">rdsd</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]));</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="p">}</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="p">}</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Classify</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" 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;">germline</span><span class="p">)</span> <span class="p">{</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Somatic mode</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bestCnOffset</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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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">somaticcnv</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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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lowestp</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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163
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<pre style="margin: 0;">+<span id="LC163" 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;">tumor</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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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">germcnv</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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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">highestprob</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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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tcnoffset</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>
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167
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<pre style="margin: 0;">+<span id="LC167" 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;">control</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>
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168
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<pre style="margin: 0;">+<span id="LC168" 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;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">normal</span> <span class="n" style="color: #333;">s1</span><span class="p">(</span><span class="n" style="color: #333;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prob1</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;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">tumor</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" 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;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">normal</span> <span class="n" style="color: #333;">s2</span><span class="p">(</span><span class="n" style="color: #333;">tumor</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">tumor</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prob2</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;">math</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">,</span> <span class="n" style="color: #333;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prob</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;">prob1</span><span class="p">,</span> <span class="n" style="color: #333;">prob2</span><span class="p">);</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prob</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;">pgerm</span><span class="p">)</span> <span class="n" style="color: #333;">germcnv</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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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Among all controls, take highest p-value (most likely germline CNV)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">highestprob</span><span class="p">)</span> <span class="n" style="color: #333;">highestprob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prob</span><span class="p">;</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="p">}</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cndiff</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;">abs</span><span class="p">(</span><span class="n" style="color: #333;">tumor</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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179
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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;">cndiff</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;">cn_offset</span><span class="p">)</span> <span class="n" style="color: #333;">germcnv</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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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Among all controls, take smallest CN difference</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">tcnoffset</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">cndiff</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tcnoffset</span><span class="p">))</span> <span class="n" style="color: #333;">tcnoffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cndiff</span><span class="p">;</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="p">}</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="p">}</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Among all tumors take best CN difference and lowest p-value</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" 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;">germcnv</span><span class="p">)</span> <span class="p">{</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">somaticcnv</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="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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">highestprob</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">lowestp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">tcnoffset</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestCnOffset</span><span class="p">))</span> <span class="p">{</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">lowestp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">highestprob</span><span class="p">;</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">bestCnOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tcnoffset</span><span class="p">;</span></span>
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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>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="p">}</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="p">}</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" 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;">somaticcnv</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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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;">_remove_info_tag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"SOMATIC"</span><span class="p">);</span></span>
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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="n" style="color: #333;">bcf_update_info_flag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"SOMATIC"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pgerm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="n" style="color: #333;">lowestp</span><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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"> <span class="n" style="color: #333;">_remove_info_tag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"PGERM"</span><span class="p">);</span></span>
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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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_float</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"PGERM"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pgerm</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cndiv</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="n" style="color: #333;">bestCnOffset</span><span class="p">;</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">_remove_info_tag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNDIFF"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_float</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNDIFF"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cndiv</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Correct CN shift</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cnmain</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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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" 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;">cncount</span><span class="p">(</span><span class="n" style="color: #333;">MAX_CN</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="p">{</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">validsite</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="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" 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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">accumulator_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">features</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">acc</span><span class="p">;</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" 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;">control</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>
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212
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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;">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;">isinf</span><span class="p">(</span><span class="n" style="color: #333;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</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;">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;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">)))</span> <span class="n" style="color: #333;">validsite</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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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">acc</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;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</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="n" style="color: #333;">control</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">validsite</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">cnshift</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">);</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cnshiftval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnshift</span><span class="p">;</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">_remove_info_tag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNSHIFT"</span><span class="p">);</span></span>
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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">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_float</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNSHIFT"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cnshiftval</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" 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;">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="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">rdcn</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;">cnshift</span><span class="p">;</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">cnval</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;">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;">rdcn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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223
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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;">cnval</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;">MAX_CN</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cncount</span><span class="p">[</span><span class="n" style="color: #333;">cnval</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]];</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Find max CN</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" 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;">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;">MAX_CN</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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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cncount</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;">cncount</span><span class="p">[</span><span class="n" style="color: #333;">cnmain</span><span class="p">])</span> <span class="n" style="color: #333;">cnmain</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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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="p">}</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="p">}</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Calculate SD</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" 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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">accumulator_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">features</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">accLocal</span><span class="p">;</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" 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;">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="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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236
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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;">cnval</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;">cnmain</span><span class="p">)</span> <span class="n" style="color: #333;">accLocal</span><span class="p">(</span><span class="n" style="color: #333;">rdcn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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237
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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">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqrt</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">accLocal</span><span class="p">));</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.025</span><span class="p">)</span> <span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.025</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cnsdval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd</span><span class="p">;</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">_remove_info_tag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNSD"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_float</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNSD"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cnsdval</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
243
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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;">cnsdval</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;">maxsd</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="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;">// Re-compute CNLs</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" 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;">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;">ftarr</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>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">altqual</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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248
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<pre style="margin: 0;">+<span id="LC248" 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;">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="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="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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">qval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_computeCNLs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">rdcn</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">sd</span><span class="p">,</span> <span class="n" style="color: #333;">cnl</span><span class="p">,</span> <span class="n" style="color: #333;">gqval</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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250
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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;">cnval</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;">ploidy</span><span class="p">)</span> <span class="n" style="color: #333;">altqual</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">qval</span><span class="p">;</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" 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;">i</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;">i</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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252
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<pre style="margin: 0;">+<span id="LC252" 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;">i</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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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="p">}</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">altqual</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;">qual</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">altqual</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;">altqual</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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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"> </span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Update QUAL and FILTER</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" 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;">altqual</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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">tmpi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_id2int</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_DT_ID</span><span class="p">,</span> <span class="s" style="color: #d14;">"PASS"</span><span class="p">);</span></span>
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260
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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;">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="mi" style="color: #099;">15</span><span class="p">)</span> <span class="n" style="color: #333;">tmpi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_id2int</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_DT_ID</span><span class="p">,</span> <span class="s" style="color: #d14;">"LowQual"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_filter</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</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;">tmpi</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Update GT fields</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" 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="k" style="font-weight: 600;">const</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;">strp</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>
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265
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<pre style="margin: 0;">+<span id="LC265" 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;">transform</span><span class="p">(</span><span class="n" style="color: #333;">ftarr</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">ftarr</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">strp</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cstyle_str</span><span class="p">());</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CN"</span><span class="p">,</span> <span class="n" style="color: #333;">cnval</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>
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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">
267
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<pre style="margin: 0;">+<span id="LC267" 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_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNL"</span><span class="p">,</span> <span class="n" style="color: #333;">cnl</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="n" style="color: #333;">MAX_CN</span><span class="p">);</span></span>
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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 class="n" style="color: #333;">bcf_update_format_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"GQ"</span><span class="p">,</span> <span class="n" style="color: #333;">gqval</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>
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<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="n" style="color: #333;">bcf_update_format_string</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"FT"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strp</span><span class="p">[</span><span class="mi" style="color: #099;">0</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>
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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="n" style="color: #333;">bcf_update_format_float</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"RDCN"</span><span class="p">,</span> <span class="n" style="color: #333;">rdcn</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>
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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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="p">}</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_write1</span><span class="p">(</span><span class="n" style="color: #333;">ofile</span><span class="p">,</span> <span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> <span class="p">}</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"></span>
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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="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>
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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svend</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;">svend</span><span class="p">);</span></span>
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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">
278
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<pre style="margin: 0;">+<span id="LC278" 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="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;">svt</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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gqval</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;">gqval</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cnval</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;">cnval</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cnl</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;">cnl</span><span class="p">);</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rdcn</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;">rdcn</span><span class="p">);</span></span>
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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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rdsd</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;">rdsd</span><span class="p">);</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"></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">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Close output VCF</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">);</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">ofile</span><span class="p">);</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Build index</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">outfile</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;">14</span><span class="p">);</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Close VCF</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_close</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// End</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" 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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298
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<pre style="margin: 0;">+<span id="LC298" 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;">"] 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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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"></span>
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300
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<pre style="margin: 0;">+<span id="LC300" 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>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"><span class="p">}</span></span>
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302
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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="LC304" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">classify</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="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">ClassifyConfig</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Define generic options</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" 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>
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309
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<pre style="margin: 0;">+<span id="LC309" 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>
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310
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<pre style="margin: 0;">+<span id="LC310" 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>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"filter,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="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="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;">filter</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;">"somatic"</span><span class="p">),</span> <span class="s" style="color: #d14;">"Filter mode (somatic, germline)"</span><span class="p">)</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" 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;">"cnv.bcf"</span><span class="p">),</span> <span class="s" style="color: #d14;">"Filtered CNV BCF output file"</span><span class="p">)</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"minsize,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;">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;">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="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;">"min. CNV size"</span><span class="p">)</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"maxsize,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;">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;">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="n" style="color: #333;">default_value</span><span class="p">(</span><span class="mi" style="color: #099;">500000000</span><span class="p">),</span> <span class="s" style="color: #d14;">"max. CNV size"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"pass,p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Filter sites for PASS"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Define somatic options</span></span>
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<pre style="margin: 0;">+<span id="LC319" 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;">somatic</span><span class="p">(</span><span class="s" style="color: #d14;">"Somatic options"</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;">somatic</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="LC321" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"samples,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;">samplefile</span><span class="p">),</span> <span class="s" style="color: #d14;">"Two-column sample file listing sample name and tumor or control"</span><span class="p">)</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"pgerm,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;">pgerm</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;">0.001</span><span class="p">),</span> <span class="s" style="color: #d14;">"probability germline"</span><span class="p">)</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"cn-offset,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;">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;">cn_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="mf" style="color: #099;">0.2</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. CN offset"</span><span class="p">)</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="p">;</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"></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;">// Define germline options</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" 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;">germline</span><span class="p">(</span><span class="s" style="color: #d14;">"Germline options"</span><span class="p">);</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">germline</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" 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>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"qual,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;">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;">c</span><span class="p">.</span><span class="n" style="color: #333;">qual</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;">50</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. site quality"</span><span class="p">)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"maxsd,x"</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;">maxsd</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;">0.15</span><span class="p">),</span> <span class="s" style="color: #d14;">"max. population SD"</span><span class="p">)</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="p">;</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Define hidden options</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" 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>
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336
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<pre style="margin: 0;">+<span id="LC336" 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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337
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<pre style="margin: 0;">+<span id="LC337" 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;">vcffile</span><span class="p">),</span> <span class="s" style="color: #d14;">"input file"</span><span class="p">)</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC339" 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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<pre style="margin: 0;">+<span id="LC340" 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>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set the visibility</span></span>
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<pre style="margin: 0;">+<span id="LC343" 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>
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344
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<pre style="margin: 0;">+<span id="LC344" 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;">somatic</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">germline</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>
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<pre style="margin: 0;">+<span id="LC345" 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>
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346
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<pre style="margin: 0;">+<span id="LC346" 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;">somatic</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">germline</span><span class="p">);</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" 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>
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348
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<pre style="margin: 0;">+<span id="LC348" 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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<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;">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>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check command line arguments</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" 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="p">{</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" 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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355
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<pre style="margin: 0;">+<span id="LC355" 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] <input.bcf>"</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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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;">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>
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357
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<pre style="margin: 0;">+<span id="LC357" 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>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Filter for PASS</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" 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;">"pass"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">filterForPass</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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362
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<pre style="margin: 0;">+<span id="LC362" 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;">filterForPass</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="LC363" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check sample file</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" 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;">tSet</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" 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;">cSet</span><span class="p">;</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" 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;">filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"somatic"</span><span class="p">)</span> <span class="p">{</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasSampleFile</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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369
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<pre style="margin: 0;">+<span id="LC369" 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;">samplefile</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;">samplefile</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;">samplefile</span><span class="p">)))</span> <span class="p">{</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="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;">"Sample 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;">samplefile</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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371
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<pre style="margin: 0;">+<span id="LC371" 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>
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372
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<pre style="margin: 0;">+<span id="LC372" 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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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get samples</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" 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;">sampleFile</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">samplefile</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;">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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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sampleFile</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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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">sampleFile</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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377
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<pre style="margin: 0;">+<span id="LC377" 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;">sampleFromFile</span><span class="p">;</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">sampleFile</span><span class="p">,</span> <span class="n" style="color: #333;">sampleFromFile</span><span class="p">);</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" 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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380
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<pre style="margin: 0;">+<span id="LC380" 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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381
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<pre style="margin: 0;">+<span id="LC381" 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;">sampleFromFile</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">);</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" 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>
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383
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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;">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>
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384
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<pre style="margin: 0;">+<span id="LC384" 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;">sample</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>
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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">
385
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<pre style="margin: 0;">+<span id="LC385" 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>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="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;">type</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="p">;</span></span>
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387
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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;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"control"</span><span class="p">)</span> <span class="n" style="color: #333;">cSet</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">);</span></span>
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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="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;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"tumor"</span><span class="p">)</span> <span class="n" style="color: #333;">tSet</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">);</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" 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;">"Sample type for "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" is neither tumor nor control"</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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391
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<pre style="margin: 0;">+<span id="LC391" 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>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="p">}</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">}</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="p">}</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="p">}</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">sampleFile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="p">}</span></span>
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398
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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;">tSet</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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399
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<pre style="margin: 0;">+<span id="LC399" 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;">"No tumor samples specified."</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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400
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<pre style="margin: 0;">+<span id="LC400" 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>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="p">}</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cSet</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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403
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<pre style="margin: 0;">+<span id="LC403" 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;">"No control samples specified."</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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404
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<pre style="margin: 0;">+<span id="LC404" 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>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="p">}</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" 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;">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;">intersection</span><span class="p">;</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" 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_intersection</span><span class="p">(</span><span class="n" style="color: #333;">cSet</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cSet</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">tSet</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">tSet</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;">back_inserter</span><span class="p">(</span><span class="n" style="color: #333;">intersection</span><span class="p">));</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" 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;">intersection</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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409
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<pre style="margin: 0;">+<span id="LC409" 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;">"Sample "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">intersection</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;">" is both a tumor and control sample."</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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410
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<pre style="margin: 0;">+<span id="LC410" 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>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="p">}</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="p">}</span> <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;">hasSampleFile</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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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check input VCF file</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" 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;">"input-file"</span><span class="p">))</span> <span class="p">{</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" 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;">vcffile</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;">vcffile</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;">vcffile</span><span class="p">)))</span> <span class="p">{</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" 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;">"Input VCF/BCF 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;">vcffile</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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419
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<pre style="margin: 0;">+<span id="LC419" 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>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="p">}</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ifile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">vcffile</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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422
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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;">ifile</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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423
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<pre style="margin: 0;">+<span id="LC423" 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;">vcffile</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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424
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<pre style="margin: 0;">+<span id="LC424" 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>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="p">}</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" 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;">bcfidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">tbx_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tbx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hts_get_format</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">format</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">vcf</span><span class="p">)</span> <span class="n" style="color: #333;">tbx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tbx_index_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">vcffile</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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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">bcfidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_index_load</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">vcffile</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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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">bcfidx</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">tbx</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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431
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<pre style="margin: 0;">+<span id="LC431" 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 file 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;">vcffile</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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432
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<pre style="margin: 0;">+<span id="LC432" 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>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="p">}</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" 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>
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436
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<pre style="margin: 0;">+<span id="LC436" 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 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;">vcffile</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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437
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<pre style="margin: 0;">+<span id="LC437" 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>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="p">}</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" 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;">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;">0</span><span class="p">))</span> <span class="p">{</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="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;">"BCF/VCF file has no sample genotypes!"</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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441
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<pre style="margin: 0;">+<span id="LC441" 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>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="p">}</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check sample names</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" 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;">filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"somatic"</span><span class="p">)</span> <span class="p">{</span></span>
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445
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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="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;">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="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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446
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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;">tSet</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">samples</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;">tSet</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">tumorSet</span><span class="p">.</span><span class="n" style="color: #333;">insert</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;">samples</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" 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;">cSet</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">samples</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;">cSet</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">controlSet</span><span class="p">.</span><span class="n" style="color: #333;">insert</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;">samples</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <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: Sample "</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;">samples</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;">" is missing in sample 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>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="p">}</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" 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;">tumorSet</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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451
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<pre style="margin: 0;">+<span id="LC451" 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;">"No tumor samples specified."</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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452
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<pre style="margin: 0;">+<span id="LC452" 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>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC454" 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;">controlSet</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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455
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<pre style="margin: 0;">+<span id="LC455" 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;">"No control samples specified."</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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456
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<pre style="margin: 0;">+<span id="LC456" 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>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="p">}</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="p">}</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcfidx</span><span class="p">)</span> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">bcfidx</span><span class="p">);</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tbx</span><span class="p">)</span> <span class="n" style="color: #333;">tbx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">tbx</span><span class="p">);</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_close</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Show cmd</span></span>
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<pre style="margin: 0;">+<span id="LC466" 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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467
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<pre style="margin: 0;">+<span id="LC467" 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>
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<pre style="margin: 0;">+<span id="LC468" 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>
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469
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<pre style="margin: 0;">+<span id="LC469" 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>
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<pre style="margin: 0;">+<span id="LC470" 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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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">classifyRun</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#6a965fc172da372b399f988708853bec938e4290"><strong>src/cnv.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,96 +16,714 @@</td>
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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 class="cp" style="color: #999; font-weight: 600;">#include <boost/accumulators/accumulators.hpp></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 <boost/accumulators/statistics.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></span>
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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/faidx.h></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/vcf.h></span></span>
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<pre style="margin: 0;"> <span id="LC24" 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="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util.h"</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>
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<pre style="margin: 0;"> <span id="LC28" 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="LC29" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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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>
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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>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SVBreakpoint</span> <span class="p">{</span></span>
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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;">pos</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;">int32_t</span> <span class="n" style="color: #333;">cilow</span><span class="p">;</span></span>
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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;">cihigh</span><span class="p">;</span></span>
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<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;">qual</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">explicit</span> <span class="n" style="color: #333;">SVBreakpoint</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;">p</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="n" style="color: #333;">p</span><span class="p">),</span> <span class="n" style="color: #333;">cilow</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">cihigh</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">qual</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="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">SVBreakpoint</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;">p</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="n" style="color: #333;">q</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="n" style="color: #333;">p</span><span class="p">),</span> <span class="n" style="color: #333;">cilow</span><span class="p">(</span><span class="n" style="color: #333;">cil</span><span class="p">),</span> <span class="n" style="color: #333;">cihigh</span><span class="p">(</span><span class="n" style="color: #333;">cih</span><span class="p">),</span> <span class="n" style="color: #333;">qual</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <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;">TSVBp</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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SortSVBreakpoint</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;">TSVBp</span><span class="p">,</span> <span class="n" style="color: #333;">TSVBp</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="LC44" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" 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;">TSVBp</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;">TSVBp</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="LC46" 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;">pos</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;">pos</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;">pos</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;">pos</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;">qual</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;">qual</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>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">BpCNV</span> <span class="p">{</span></span>
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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;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" 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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<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>
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<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>
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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;">ciendlow</span><span class="p">;</span></span>
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<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>
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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>
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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>
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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>
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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="LC54" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">zscore</span><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="n" style="color: #333;">BpCNV</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;">double</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">z</span><span class="p">)</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;">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;">zscore</span><span class="p">(</span><span class="n" style="color: #333;">z</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC58" 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="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC60" 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="LC61" 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="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">mergeCNVs</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;">CNV</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">chrcnv</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;">CNV</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">cnvs</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="c1" style="color: #998; font-style: italic;">// Merge neighboring segments if too similar</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;">bool</span> <span class="n" style="color: #333;">merged</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="LC65" 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;">CNV</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">newcnv</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">merged</span><span class="p">)</span> <span class="p">{</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <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="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="LC68" 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="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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="n" style="color: #333;">chrcnv</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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69
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<pre style="margin: 0;">+<span id="LC69" 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;">k</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">k</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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71
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<pre style="margin: 0;">+<span id="LC71" 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;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</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;">chrcnv</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;">j</span><span class="p">)</span> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">allValid</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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73
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<pre style="margin: 0;">+<span id="LC73" 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;">pre</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;">pre</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pre</span><span class="p">)</span> <span class="p">{</span></span>
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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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">diff</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;">abs</span><span class="p">(</span><span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">pre</span><span class="p">].</span><span class="n" style="color: #333;">cn</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">cn</span><span class="p">);</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">diff</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;">cn_offset</span><span class="p">)</span> <span class="p">{</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">allValid</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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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="p">}</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="p">}</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allValid</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;">j</span><span class="p">;</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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53
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="p">}</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="p">};</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp"> </span>
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83
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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;">k</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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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Merge</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" 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="p">(</span><span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cn</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">cn</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">2.0</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;">double</span> <span class="n" style="color: #333;">mp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mappable</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">mappable</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">2.0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">newcnv</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">CNV</span><span class="p">(</span><span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">chrcnv</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 class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciposlow</span><span class="p">,</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciposhigh</span><span class="p">,</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">ciendlow</span><span class="p">,</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">ciendhigh</span><span class="p">,</span> <span class="n" style="color: #333;">cn</span><span class="p">,</span> <span class="n" style="color: #333;">mp</span><span class="p">));</span> </span>
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<pre style="margin: 0;">+<span id="LC88" 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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">newcnv</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="p">}</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="p">}</span></span>
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92
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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;">newcnv</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;">chrcnv</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="n" style="color: #333;">merged</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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93
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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="p">{</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">chrcnv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newcnv</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">newcnv</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="p">}</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Insert into global CNV vector</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" 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;">chrcnv</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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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">chrcnv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << chrcnv[i].chr << '\t' << chrcnv[i].start << '\t' << chrcnv[i].end << "\tMerged" << std::endl;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="p">}</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="p">}</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC107" 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 class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TGenomicBreakpoints</span><span class="p">></span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" 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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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">breakpointRefinement</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="n" style="color: #333;">TGenomicBreakpoints</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">svbp</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;">CNV</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">cnvs</span><span class="p">)</span> <span class="p">{</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" 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;">TGenomicBreakpoints</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">TSVs</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> </span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Estimate CN shift</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" 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;">n</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;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cnvs</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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">cnvs</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="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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">refIndex</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="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 class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">precovsum</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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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">preexpcov</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="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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">succovsum</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="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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sucexpcov</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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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <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;">cnvs</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="n" style="color: #333;">start</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" 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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">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="p">{</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" 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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122
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<pre style="margin: 0;">+<span id="LC122" 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;">cnvs</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="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">precovsum</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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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">preexpcov</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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125
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<pre style="margin: 0;">+<span id="LC125" 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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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">succovsum</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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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">sucexpcov</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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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="p">}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" 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>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="p">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">precndiff</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;">abs</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;">precovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">preexpcov</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;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">succovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sucexpcov</span><span class="p">));</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Intersect with delly SVs</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">searchWindow</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="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">ciposlow</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="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">ciposhigh</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">));</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <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;">const_iterator</span> <span class="n" style="color: #333;">itbest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">svbp</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>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Current CNV start for this breakpoint</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <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;">const_iterator</span> <span class="n" style="color: #333;">itsv</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;">svbp</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;">svbp</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;">SVBreakpoint</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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">searchWindow</span><span class="p">)),</span> <span class="n" style="color: #333;">SortSVBreakpoint</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SVBreakpoint</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</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;">svbp</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;">itsv</span><span class="p">)</span> <span class="p">{</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" 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;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">searchWindow</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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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">
141
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<pre style="margin: 0;">+<span id="LC141" 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;">pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">end</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="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">
142
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<pre style="margin: 0;">+<span id="LC142" 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;">pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">cnvs</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="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="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="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">itbest</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">svbp</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;">itsv</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;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">))</span> <span class="n" style="color: #333;">itbest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itsv</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <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">
145
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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;">itbest</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">svbp</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;">itbest</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="mi" style="color: #099;">50</span><span class="p">))</span> <span class="p">{</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check refined CNV</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">precovsum</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="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">preexpcov</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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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">succovsum</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">sucexpcov</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="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">
151
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<pre style="margin: 0;">+<span id="LC151" 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;">cnvs</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="n" style="color: #333;">start</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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">
152
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<pre style="margin: 0;">+<span id="LC152" 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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">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="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">
153
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<pre style="margin: 0;">+<span id="LC153" 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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154
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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;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">itbest</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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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">precovsum</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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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">preexpcov</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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157
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<pre style="margin: 0;">+<span id="LC157" 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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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">succovsum</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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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">sucexpcov</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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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="p">}</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" 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>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="p">}</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">postcndiff</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;">abs</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;">precovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">preexpcov</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;">ploidy</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">succovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sucexpcov</span><span class="p">));</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << cnvs[n-1].end << ',' << itbest->pos << ',' << precndiff << ',' << postcndiff << std::endl;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">precndiff</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">postcndiff</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;">cn_offset</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;">abs</span><span class="p">(</span><span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">50000</span><span class="p">))</span> <span class="p">{</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Accept new breakpoint</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</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="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</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="n" style="color: #333;">ciendlow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itbest</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;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cilow</span><span class="p">;</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</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="n" style="color: #333;">ciendhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itbest</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;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cihigh</span><span class="p">;</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">ciposlow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itbest</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;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cilow</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">ciposhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itbest</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;">itbest</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cihigh</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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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <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>
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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="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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181
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<pre style="margin: 0;"> <span id="LC181" 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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64
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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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65
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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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66
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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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67
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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>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">breakpointRefinement2</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="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;">CNV</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">cnvs</span><span class="p">)</span> <span class="p">{</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"></span>
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184
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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;">maxbpshift</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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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> </span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Breakpoint refinement</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" 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;">n</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;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cnvs</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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">prehalf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cnvs</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="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cnvs</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="n" style="color: #333;">end</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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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="n" style="color: #333;">prehalf</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;">cnvs</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="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">maxbpshift</span><span class="p">,</span> <span class="n" style="color: #333;">prehalf</span><span class="p">);</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">suchalf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">2</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="n" style="color: #333;">suchalf</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">maxbpshift</span><span class="p">,</span> <span class="n" style="color: #333;">suchalf</span><span class="p">);</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">precovsum</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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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">preexpcov</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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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">succovsum</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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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;">double</span> <span class="n" style="color: #333;">sucexpcov</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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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <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;">cnvs</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="n" style="color: #333;">start</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" 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;">validpos</span><span class="p">;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">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="p">{</span></span>
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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">
199
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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;">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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200
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<pre style="margin: 0;">+<span id="LC200" 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;">prehalf</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">precovsum</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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<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 class="n" style="color: #333;">preexpcov</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="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">
203
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<pre style="margin: 0;">+<span id="LC203" 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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204
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<pre style="margin: 0;">+<span id="LC204" 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;">suchalf</span><span class="p">)</span> <span class="n" style="color: #333;">validpos</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">succovsum</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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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">sucexpcov</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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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="p">}</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="p">}</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" 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>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="p">}</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">precn</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;">precovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">preexpcov</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">succn</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;">succovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sucexpcov</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Shift Bp</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" 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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">diffcn</span><span class="p">(</span><span class="n" style="color: #333;">validpos</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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215
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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;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">validpos</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;">idx</span><span class="p">)</span> <span class="p">{</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">preexpcov</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;">sucexpcov</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="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">precn</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;">precovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">preexpcov</span><span class="p">;</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="n" style="color: #333;">succn</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;">succovsum</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sucexpcov</span><span class="p">;</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="n" style="color: #333;">diffcn</span><span class="p">[</span><span class="n" style="color: #333;">idx</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;">abs</span><span class="p">(</span><span class="n" style="color: #333;">precn</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">succn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (validpos[idx] == cnvs[n-1].end) std::cerr << "-->";</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << validpos[idx] << ',' << precn << ',' << succn << ',' << diffcn[idx] << std::endl;</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 class="c1" style="color: #998; font-style: italic;">// Add to pre, remove from suc</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">precovsum</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;">validpos</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="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">preexpcov</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;">validpos</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]]].</span><span class="n" style="color: #333;">coverage</span><span class="p">;</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">succovsum</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;">validpos</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="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">sucexpcov</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;">validpos</span><span class="p">[</span><span class="n" style="color: #333;">idx</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="LC228" class="line" lang="cpp"> <span class="p">}</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Find best</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">bestIdx</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>
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231
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<pre style="margin: 0;">+<span id="LC231" 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;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">validpos</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;">idx</span><span class="p">)</span> <span class="p">{</span></span>
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232
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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;">bestIdx</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">diffcn</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">diffcn</span><span class="p">[</span><span class="n" style="color: #333;">bestIdx</span><span class="p">]))</span> <span class="n" style="color: #333;">bestIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="p">}</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bestIdx</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="p">{</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Update breakpoint</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</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="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">validpos</span><span class="p">[</span><span class="n" style="color: #333;">bestIdx</span><span class="p">];</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">validpos</span><span class="p">[</span><span class="n" style="color: #333;">bestIdx</span><span class="p">];</span></span>
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68
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="p">}</span></span>
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t n = 0; n < cnvs.size(); ++n) std::cerr << hdr->target_name[cnvs[n].chr] << '\t' << cnvs[n].start << '\t' << cnvs[n].end << "\tRefinement" << std::endl;</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="p">}</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> </span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"></span>
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244
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<pre style="margin: 0;">+<span id="LC244" 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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245
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<pre style="margin: 0;">+<span id="LC245" 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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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">genotypeCNVs</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="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;">CNV</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">cnvs</span><span class="p">)</span> <span class="p">{</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" 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;">n</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;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cnvs</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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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248
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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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">refIndex</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" 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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250
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<pre style="margin: 0;">+<span id="LC250" 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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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_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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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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="LC253" 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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">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="p">{</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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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255
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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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256
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<pre style="margin: 0;">+<span id="LC256" 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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257
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<pre style="margin: 0;">+<span id="LC257" 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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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="p">}</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" 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>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="p">}</span></span>
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261
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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;">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="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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 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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<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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mp</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="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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">cn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cn</span><span class="p">;</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">mappable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mp</span><span class="p">;</span></span>
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70
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"></span>
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71
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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>
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72
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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 old old_line" data-linenumber="73" 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">
73
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<td class="diff-line-num new_line old" data-linenumber="267" 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="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>
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74
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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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<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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<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>
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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>
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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>
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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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<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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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Estimate SD</span></span>
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<pre style="margin: 0;">+<span id="LC268" 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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">accumulator_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">features</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">acc</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">wsz</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="mi" style="color: #099;">10</span><span class="p">;</span></span>
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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;">wsz</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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271
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<pre style="margin: 0;">+<span id="LC271" 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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272
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<pre style="margin: 0;">+<span id="LC272" 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="LC273" 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="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" 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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" 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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</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;">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="p">{</span></span>
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83
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276
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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;">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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84
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277
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<pre style="margin: 0;"> <span id="LC277" 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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85
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278
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<pre style="margin: 0;"> <span id="LC278" 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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86
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279
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<pre style="margin: 0;"> <span id="LC279" 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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280
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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;">winlen</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">wsz</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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281
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<pre style="margin: 0;">+<span id="LC281" 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="p">;</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 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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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">acc</span><span class="p">(</span><span class="n" style="color: #333;">cn</span><span class="p">);</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" 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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285
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<pre style="margin: 0;">+<span id="LC285" 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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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="p">}</span></span>
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287
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<pre style="margin: 0;"> <span id="LC287" 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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89
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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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90
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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="LC288" 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>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="p">}</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sqrt</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">acc</span><span class="p">));</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.025</span><span class="p">)</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.025</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="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="LC293" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Invalid</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">cn</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>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.025</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="p">}</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="p">}</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="p">}</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> </span>
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300
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<pre style="margin: 0;">+<span id="LC300" 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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301
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<pre style="margin: 0;">+<span id="LC301" 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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302
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<pre style="margin: 0;">+<span id="LC302" 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="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;">CNV</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">cnvs</span><span class="p">)</span> <span class="p">{</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parameters</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">smallestWin</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;">minCnvSize</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">biggestWin</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="mi" style="color: #099;">200</span><span class="p">;</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">chain</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Find breakpoints</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" 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;">BpCNV</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bpmax</span><span class="p">;</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpmax</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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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Scanning window sizes</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" 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;">winsize</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">wsize</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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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">wsize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">biggestWin</span><span class="p">)</span> <span class="p">{</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">winsize</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">wsize</span><span class="p">);</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">wsize</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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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="p">}</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate window sizes</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">TCnVal</span><span class="p">;</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" 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;">TCnVal</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TCN</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" 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;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TChrPos</span><span class="p">;</span></span>
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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">
324
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<pre style="margin: 0;">+<span id="LC324" 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;">BpCNV</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bpvec</span><span class="p">;</span></span>
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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">
325
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<pre style="margin: 0;">+<span id="LC325" 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;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">winsize</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;">idx</span><span class="p">)</span> <span class="p">{</span></span>
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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">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">idxOffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">winsize</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">winsize</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="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">
327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << idx << ',' << winsize[idx] << ',' << idxOffset << ',' << bpvec.size() << ',' << hdr->target_len[refIndex] << std::endl;</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="n" style="color: #333;">TCN</span> <span class="n" style="color: #333;">cnvec</span><span class="p">;</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">TChrPos</span> <span class="n" style="color: #333;">wpos</span><span class="p">;</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">wstart</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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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">wstart</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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332
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<pre style="margin: 0;">+<span id="LC332" 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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333
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<pre style="margin: 0;">+<span id="LC333" 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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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_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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335
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<pre style="margin: 0;">+<span id="LC335" 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="n" style="color: #333;">wstart</span><span class="p">;</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</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;">winsize</span><span class="p">[</span><span class="n" style="color: #333;">idx</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="p">{</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" 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="LC338" 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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339
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<pre style="margin: 0;">+<span id="LC339" 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="LC340" 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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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="p">}</span></span>
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342
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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;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="p">}</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" 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;">winsize</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">])</span> <span class="p">{</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Full window</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 class="n" style="color: #333;">cnvec</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;">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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<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">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cnvec</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;">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="mf" style="color: #099;">100.0</span><span class="p">));</span></span>
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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">
348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">wpos</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">wstart</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">wstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Identify breakpoints</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">TCN</span> <span class="n" style="color: #333;">pre</span><span class="p">(</span><span class="n" style="color: #333;">chain</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="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">TCN</span> <span class="n" style="color: #333;">suc</span><span class="p">(</span><span class="n" style="color: #333;">chain</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="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">TChrPos</span> <span class="n" style="color: #333;">prep</span><span class="p">(</span><span class="n" style="color: #333;">chain</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="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">TChrPos</span> <span class="n" style="color: #333;">sucp</span><span class="p">(</span><span class="n" style="color: #333;">chain</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="LC358" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">idxbp</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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359
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<pre style="margin: 0;">+<span id="LC359" 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;">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>
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<pre style="margin: 0;">+<span id="LC360" 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;">chain</span><span class="p">)</span> <span class="p">{</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">pre</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;">chain</span><span class="p">]</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;">k</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">prep</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;">chain</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wpos</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" 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="mi" style="color: #099;">1</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;">size</span><span class="p">())</span> <span class="p">{</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" 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="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">bpvec</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BpCNV</span><span class="p">(</span><span class="n" style="color: #333;">wpos</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">],</span> <span class="n" style="color: #333;">wpos</span><span class="p">[</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 class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">idxbp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">idxOffset</span><span class="p">;</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="p">}</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" 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;">k</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="n" style="color: #333;">chain</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">suc</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;">chain</span><span class="p">]</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;">k</span><span class="p">];</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">sucp</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;">chain</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wpos</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Midpoint</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="n" style="color: #333;">TCnVal</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suc</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;">chain</span><span class="p">];</span> </span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <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;">sucp</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;">chain</span><span class="p">];</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">posNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sucp</span><span class="p">[(</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 class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">chain</span><span class="p">];</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">suc</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;">chain</span><span class="p">]</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;">k</span><span class="p">];</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">sucp</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;">chain</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wpos</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> </span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Debug</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t m = 0; m < pre.size(); ++m) std::cerr << prep[m] << '\t' << pre[m] << std::endl;</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "M:" << pos << '\t' << val << std::endl;</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t m = 0; m < suc.size(); ++m) std::cerr << sucp[m] << '\t' << suc[m] << std::endl;</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> </span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Any shift in CN?</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" 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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">accumulator_set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCnVal</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">features</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">accpre</span><span class="p">;</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" 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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">accumulator_set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TCnVal</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">features</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">accsuc</span><span class="p">;</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" 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;">m</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;">m</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pre</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;">m</span><span class="p">)</span> <span class="n" style="color: #333;">accpre</span><span class="p">(</span><span class="n" style="color: #333;">pre</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">]);</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" 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;">m</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;">m</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">suc</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;">m</span><span class="p">)</span> <span class="n" style="color: #333;">accsuc</span><span class="p">(</span><span class="n" style="color: #333;">suc</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">]);</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">diff</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;">abs</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">accsuc</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">accpre</span><span class="p">));</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Breakpoint candidate</span></span>
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390
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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;">zscore</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="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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">diff</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;">stringency</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sqrt</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">accpre</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">diff</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;">stringency</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sqrt</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">accsuc</span><span class="p">))))</span> <span class="p">{</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">zscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diff</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;">sqrt</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">accpre</span><span class="p">)),</span> <span class="n" style="color: #333;">sqrt</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;">accumulators</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">variance</span><span class="p">(</span><span class="n" style="color: #333;">accsuc</span><span class="p">)));</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">}</span></span>
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394
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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;">idx</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;">bpvec</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BpCNV</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">posNext</span><span class="p">,</span> <span class="n" style="color: #333;">zscore</span><span class="p">));</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" 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;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idxbp</span><span class="p">;</span> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">idxbp</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">idxOffset</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">sub</span><span class="p">)</span> <span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">sub</span><span class="p">].</span><span class="n" style="color: #333;">zscore</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">zscore</span><span class="p">;</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">idxbp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">idxOffset</span><span class="p">;</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="p">}</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">pre</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;">chain</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">prep</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;">chain</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>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="p">}</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Local maxima</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpvec</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <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;">bpvec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">posNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpvec</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>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">bestDiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">zscore</span><span class="p">;</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" 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;">n</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;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bpvec</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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "B:" << bpvec[n].start << '-' << bpvec[n].end << ':' << bpvec[n].zscore << std::endl;</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">zscore</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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413
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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;">bestDiff</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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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "M:" << pos << '-' << posNext << ':' << bestDiff << std::endl;</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">bpmax</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BpCNV</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">posNext</span><span class="p">,</span> <span class="n" style="color: #333;">bestDiff</span><span class="p">));</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" 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;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">posNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</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="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">bestDiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">zscore</span><span class="p">;</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC420" 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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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">zscore</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bestDiff</span><span class="p">)</span> <span class="p">{</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Replace local max</span></span>
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<pre style="margin: 0;">+<span id="LC423" 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;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</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="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">posNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</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="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">bestDiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">zscore</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 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;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">].</span><span class="n" style="color: #333;">zscore</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bestDiff</span><span class="p">)</span> <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;">// Extend local max</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">posNext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpvec</span><span class="p">[</span><span class="n" style="color: #333;">n</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="LC429" 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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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"></span>
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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>
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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>
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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>
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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>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Breakpoints</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" 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;">n</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;">n</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">bpmax</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;">n</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cil</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="LC438" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cih</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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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="n" style="color: #333;">cil</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpmax</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="n" style="color: #333;">start</span><span class="p">;</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">cih</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpmax</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="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="p">}</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cel</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ceh</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bpmax</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">cel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpmax</span><span class="p">[</span><span class="n" style="color: #333;">n</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="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">ceh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpmax</span><span class="p">[</span><span class="n" style="color: #333;">n</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="LC448" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << (cih - cil) << ';' << (ceh - cel) << std::endl;</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cnvstart</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;">cil</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cih</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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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cnvend</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;">cel</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ceh</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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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">estcnvstart</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>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">estcnvend</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>
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454
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<pre style="margin: 0;">+<span id="LC454" 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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455
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<pre style="margin: 0;">+<span id="LC455" 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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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_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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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <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;">cnvstart</span><span class="p">;</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" 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;">cnvend</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="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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459
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<pre style="margin: 0;">+<span id="LC459" 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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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">estcnvstart</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="n" style="color: #333;">estcnvstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">estcnvend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" 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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463
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<pre style="margin: 0;">+<span id="LC463" 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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464
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<pre style="margin: 0;">+<span id="LC464" 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="LC465" class="line" lang="cpp"> <span class="p">}</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" 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>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="p">}</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">estcnvstart</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="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">estcnvend</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="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">estcnvend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">estcnvstart</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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469
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<pre style="margin: 0;">+<span id="LC469" 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="p">;</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 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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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mp</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="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;">estcnvend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">estcnvstart</span><span class="p">);</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">CNV</span><span class="p">(</span><span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="n" style="color: #333;">estcnvstart</span><span class="p">,</span> <span class="n" style="color: #333;">estcnvend</span><span class="p">,</span> <span class="n" style="color: #333;">cil</span><span class="p">,</span> <span class="n" style="color: #333;">cih</span><span class="p">,</span> <span class="n" style="color: #333;">cel</span><span class="p">,</span> <span class="n" style="color: #333;">ceh</span><span class="p">,</span> <span class="n" style="color: #333;">cn</span><span class="p">,</span> <span class="n" style="color: #333;">mp</span><span class="p">));</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << hdr->target_name[refIndex] << '\t' << estcnvstart << '\t' << estcnvend << '\t' << '(' << cil << ',' << cih << ')' << '\t' << '(' << cel << ',' << ceh << ')' << '\t' << cn << '\t' << mp << std::endl;</span></span>
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104
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"> <span class="p">}</span></span>
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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>
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106
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475
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp"> <span class="p">}</span></span>
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse Delly CNV VCF file</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" 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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481
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<pre style="margin: 0;">+<span id="LC481" 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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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="n" style="color: #333;">parseVcfCNV</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;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hd</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;">CNV</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">cnvs</span><span class="p">)</span> <span class="p">{</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Load bcf file</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ifile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genofile</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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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf1_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;">bcf_init</span><span class="p">();</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse bcf</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nsvend</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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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <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;">svend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ncipos</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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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <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;">cipos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nmp</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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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nsvt</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="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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nmethod</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="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 class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">wimethod</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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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</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="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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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_unpack</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_UN_INFO</span><span class="p">);</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Delly BCF file?</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" 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;">wimethod</span><span class="p">)</span> <span class="p">{</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">wimethod</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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506
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<pre style="margin: 0;">+<span id="LC506" 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_string</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;">"SVMETHOD"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nmethod</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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507
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<pre style="margin: 0;">+<span id="LC507" 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;">mstr</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;">method</span><span class="p">);</span></span>
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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="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">mstr</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;">10</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">mstr</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"EMBL.DELLY"</span><span class="p">))</span> <span class="n" style="color: #333;">wimethod</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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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="p">}</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="p">}</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"></span>
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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">
512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Delly</span></span>
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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">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wimethod</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 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">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Fill SV record</span></span>
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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">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">CNV</span> <span class="n" style="color: #333;">cnv</span><span class="p">;</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" 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="n" style="color: #333;">bcf_hdr_id2name</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rid</span><span class="p">);</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" 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;">hd</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>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</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;">tid</span><span class="p">;</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</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;">rec</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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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">qval</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;">qual</span><span class="p">;</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"></span>
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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;">// Parse CNV type</span></span>
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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="n" style="color: #333;">bcf_get_info_string</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;">"SVTYPE"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">svt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nsvt</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="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="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;">"CNV"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> </span>
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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;">// Parse INFO</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" 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;">"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;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">end</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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<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="k" style="font-weight: 600;">else</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="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="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;">"CIPOS"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cipos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ncipos</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="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="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciposlow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</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;">cipos</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciposhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</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;">cipos</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" 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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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciposlow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciposhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="p">}</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" 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;">"CIEND"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cipos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ncipos</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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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciendlow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</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;">cipos</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciendhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</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;">cipos</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" 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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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciendlow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">ciendhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="p">}</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" 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_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;">"MP"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</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;">nmp</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;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">mappable</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mp</span><span class="p">;</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">cnv</span><span class="p">.</span><span class="n" style="color: #333;">mappable</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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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">cnv</span><span class="p">);</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="p">}</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="p">}</span></span>
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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;">// Clean-up</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">svend</span><span class="p">);</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">svt</span><span class="p">);</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">method</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">cipos</span><span class="p">);</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">);</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"> </span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Close VCF</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_close</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="p">}</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"></span>
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108
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> </span>
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564
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<pre style="margin: 0;">+<span id="LC564" 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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565
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<pre style="margin: 0;">+<span id="LC565" 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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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvVCF</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;">CNV</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;">cnvs</span><span class="p">)</span> <span class="p">{</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open one bam file header</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" 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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569
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<pre style="margin: 0;">+<span id="LC569" 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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570
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<pre style="margin: 0;">+<span id="LC570" 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;">bamhd</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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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output all copy-number variants</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">cnvfile</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;">"wb"</span><span class="p">);</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">bcf_hdr_init</span><span class="p">(</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"></span>
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<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="c1" style="color: #998; font-style: italic;">// Print vcf header</span></span>
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<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="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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<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;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">gregorian</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">date</span> <span class="n" style="color: #333;">today</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">now</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">();</span></span>
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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="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;">datestr</span><span class="p">(</span><span class="s" style="color: #d14;">"##fileDate="</span><span class="p">);</span></span>
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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="n" style="color: #333;">datestr</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;">gregorian</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_iso_string</span><span class="p">(</span><span class="n" style="color: #333;">today</span><span class="p">);</span></span>
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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;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">datestr</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 old_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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<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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##ALT=<ID=CNV,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">copy-number variants</span><span class="se" style="color: #d14;">\"</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="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">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FILTER=<ID=LowQual,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Poor quality copy-number variant</span><span class="se" style="color: #d14;">\"</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="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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<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
</td>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=CIEND,Number=2,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Confidence interval around END</span><span class="se" style="color: #d14;">\"</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="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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<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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=CIPOS,Number=2,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Confidence interval around POS</span><span class="se" style="color: #d14;">\"</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="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">
</td>
<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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=END,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">End position of the copy-number variant</span><span class="se" style="color: #d14;">\"</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="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">
</td>
<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">
587
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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="LC587" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=MP,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Mappable fraction of CNV</span><span class="se" style="color: #d14;">\"</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="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">
</td>
<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;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Imprecise copy-number variant</span><span class="se" style="color: #d14;">\"</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="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">
</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
</td>
<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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SVTYPE,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type of structural variant</span><span class="se" style="color: #d14;">\"</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="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">
</td>
<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SVMETHOD,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type of approach used to detect CNV</span><span class="se" style="color: #d14;">\"</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="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">
</td>
<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
591
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=GT,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Genotype</span><span class="se" style="color: #d14;">\"</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="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">
</td>
<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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=CN,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Integer copy-number</span><span class="se" style="color: #d14;">\"</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="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">
593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=CNL,Number=.,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Log10-scaled copy-number likelihoods</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Genotype Quality</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=FT,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Per-sample genotype filter</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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">
596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=RDCN,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Read-depth based copy-number estimate</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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 class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=RDSD,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Read-depth standard deviation</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add reference</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" 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;">refloc</span><span class="p">(</span><span class="s" style="color: #d14;">"##reference="</span><span class="p">);</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> <span class="n" style="color: #333;">refloc</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>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">refloc</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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604
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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;">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;">bamhd</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;">i</span><span class="p">)</span> <span class="p">{</span></span>
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605
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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;">refname</span><span class="p">(</span><span class="s" style="color: #d14;">"##contig=<ID="</span><span class="p">);</span></span>
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<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="n" style="color: #333;">refname</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;">bamhd</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;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">",length="</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="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="p">(</span><span class="n" style="color: #333;">bamhd</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;">i</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>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">refname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="p">}</span></span>
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<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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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add samples</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_add_sample</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">sampleName</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="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_add_sample</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_hdr_write</span><span class="p">(</span><span class="n" style="color: #333;">fp</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;">0</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: Failed to write BCF header!"</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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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cnvid</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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615
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<pre style="margin: 0;">+<span id="LC615" 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;">cnvs</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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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Genotype arrays</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <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;">gts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</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="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <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;">gqval</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <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;">cnval</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cnrdval</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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="n" style="color: #333;">malloc</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cnsdval</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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="n" style="color: #333;">malloc</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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cnl</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</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="n" style="color: #333;">malloc</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="n" style="color: #333;">MAX_CN</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">));</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"></span>
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624
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<pre style="margin: 0;">+<span id="LC624" 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;">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;">ftarr</span><span class="p">;</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">ftarr</span><span class="p">.</span><span class="n" style="color: #333;">resize</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>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> </span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate all structural variants</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" 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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629
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<pre style="margin: 0;">+<span id="LC629" 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;">"Genotyping"</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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630
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<pre style="margin: 0;">+<span id="LC630" 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;">cnvs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">);</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf1_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;">bcf_init</span><span class="p">();</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" 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;">cnvs</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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633
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<pre style="margin: 0;">+<span id="LC633" 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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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Invalid CNV?</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cn</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>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Integer copy-number</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">absCN</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cn</span><span class="p">);</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" 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;">segmentation</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">absCN</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="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> </span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output main vcf fields</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" 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;">rid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_name2id</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">bamhd</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr</span><span class="p">]);</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">svStartPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnvs</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">svEndPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnvs</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="p">;</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svEndPos</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;">bamhd</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr</span><span class="p">])</span> <span class="n" style="color: #333;">svEndPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamhd</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"> <span class="n" style="color: #333;">rec</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;">svStartPos</span><span class="p">;</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" 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;">id</span><span class="p">(</span><span class="s" style="color: #d14;">"CNV"</span><span class="p">);</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" 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;">padNumber</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="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="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cnvid</span><span class="p">);</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"> <span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">(),</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">);</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">padNumber</span><span class="p">;</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_id</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;">id</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" 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="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CNV"</span><span class="p">;</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" 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;">alleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"N,<"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">">"</span><span class="p">;</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_alleles_str</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;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> </span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add INFO fields</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_flag</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;">"IMPRECISE"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_string</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;">"SVTYPE"</span><span class="p">,</span> <span class="n" style="color: #333;">svtype</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="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;">dellyVersion</span><span class="p">(</span><span class="s" style="color: #d14;">"EMBL.DELLYv"</span><span class="p">);</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="n" style="color: #333;">dellyVersion</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dellyVersionNumber</span><span class="p">;</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_string</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;">"SVMETHOD"</span><span class="p">,</span> <span class="n" style="color: #333;">dellyVersion</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">tmpi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">svEndPos</span><span class="p">;</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_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;">"END"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmpi</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ciend</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="n" style="color: #333;">ciend</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciendlow</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cnvs</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="p">;</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">ciend</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="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciendhigh</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cnvs</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="p">;</span></span>
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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">
669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cipos</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="n" style="color: #333;">cipos</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciposlow</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cnvs</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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<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 class="n" style="color: #333;">cipos</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="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciposhigh</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cnvs</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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<td class="diff-line-num new new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_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;">"CIPOS"</span><span class="p">,</span> <span class="n" style="color: #333;">cipos</span><span class="p">,</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="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_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;">"CIEND"</span><span class="p">,</span> <span class="n" style="color: #333;">ciend</span><span class="p">,</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="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">
674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">tmpf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mappable</span><span class="p">;</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_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;">"MP"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmpf</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Genotyping</span></span>
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<td class="diff-line-num new new_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;">cnval</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;">absCN</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="n" style="color: #333;">cnrdval</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cn</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"> <span class="n" style="color: #333;">cnsdval</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;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sd</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="n" style="color: #333;">gts</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;">bcf_gt_missing</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="n" style="color: #333;">gts</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="n" style="color: #333;">bcf_gt_missing</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">qval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_computeCNLs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">cn</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">sd</span><span class="p">,</span> <span class="n" style="color: #333;">cnl</span><span class="p">,</span> <span class="n" style="color: #333;">gqval</span><span class="p">);</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" 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;">hasGenoFile</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;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnvs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">qval</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Leave site quality in genotyping mode</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <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;">qval</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">tmpi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_id2int</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_DT_ID</span><span class="p">,</span> <span class="s" style="color: #d14;">"PASS"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
687
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<pre style="margin: 0;">+<span id="LC687" 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;">qual</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;">tmpi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_id2int</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_DT_ID</span><span class="p">,</span> <span class="s" style="color: #d14;">"LowQual"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_filter</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmpi</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> </span>
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690
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<pre style="margin: 0;">+<span id="LC690" 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="mi" style="color: #099;">0</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="mi" style="color: #099;">0</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 new new_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
691
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<pre style="margin: 0;">+<span id="LC691" 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="mi" style="color: #099;">0</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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<td class="diff-line-num new new_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="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="k" style="font-weight: 600;">const</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;">strp</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>
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<td class="diff-line-num new new_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">ftarr</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">ftarr</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">strp</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cstyle_str</span><span class="p">());</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="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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<td class="diff-line-num new new_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"CN"</span><span class="p">,</span> <span class="n" style="color: #333;">cnval</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>
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<td class="diff-line-num new new_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="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;">"CNL"</span><span class="p">,</span> <span class="n" style="color: #333;">cnl</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="n" style="color: #333;">MAX_CN</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"GQ"</span><span class="p">,</span> <span class="n" style="color: #333;">gqval</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>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_string</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;">"FT"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strp</span><span class="p">[</span><span class="mi" style="color: #099;">0</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>
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<td class="diff-line-num new new_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="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;">"RDCN"</span><span class="p">,</span> <span class="n" style="color: #333;">cnrdval</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>
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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;">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;">"RDSD"</span><span class="p">,</span> <span class="n" style="color: #333;">cnsdval</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>
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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;">bcf_write1</span><span class="p">(</span><span class="n" style="color: #333;">fp</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>
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<td class="diff-line-num new new_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_clear1</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="p">}</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="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;">// Clean-up</span></span>
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<td class="diff-line-num new new_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">gts</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">gqval</span><span class="p">);</span></span>
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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="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">cnval</span><span class="p">);</span></span>
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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="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">cnrdval</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">cnsdval</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">cnl</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="p">}</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Close BAM file</span></span>
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<td class="diff-line-num new new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">bamhd</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
717
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<pre style="margin: 0;">+<span id="LC717" 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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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Close VCF file</span></span>
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<td class="diff-line-num new new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Build index</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">cnvfile</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;">14</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#dcad3ddfd75218047069bbaa2acab307a0655169"><strong>src/coral.h</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">@@ -25,17 +25,20 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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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>
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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>
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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>
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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;">hasStatsFile</span><span class="p">;</span></span>
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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;">hasBedFile</span><span class="p">;</span></span>
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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;">hasScanFile</span><span class="p">;</span></span>
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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;">noScanWindowSelection</span><span class="p">;</span></span>
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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;">segmentation</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;">bool</span> <span class="n" style="color: #333;">hasGenoFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" 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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<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;">nchr</span><span class="p">;</span></span>
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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;">meanisize</span><span class="p">;</span></span>
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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;">window_size</span><span class="p">;</span></span>
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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;">window_offset</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" 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>
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<pre style="margin: 0;"> <span id="LC40" 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>
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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;">minCnvSize</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;">uint16_t</span> <span class="n" style="color: #333;">minQual</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;">uint16_t</span> <span class="n" style="color: #333;">mad</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" 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>
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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">@@ -44,9 +47,13 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC47" 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>
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<pre style="margin: 0;"> <span id="LC48" 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>
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<pre style="margin: 0;"> <span id="LC49" 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>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">stringency</span><span class="p">;</span></span>
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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;">cn_offset</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" 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>
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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>
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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>
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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;">vcffile</span><span class="p">;</span></span>
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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;">genofile</span><span class="p">;</span></span>
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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;">cnvfile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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;">covfile</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" 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="LC58" 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>
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<pre style="margin: 0;"> <span id="LC59" 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>
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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">@@ -54,7 +61,7 @@ namespace torali</td>
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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;">bedFile</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;">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>
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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="LC57" class="line" lang="cpp"></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;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">CountDNAConfigLib</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;">uint16_t</span> <span class="n" style="color: #333;">madCutoff</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;">uint16_t</span> <span class="n" style="color: #333;">madNormalCutoff</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">@@ -90,13 +97,25 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open output files</span></span>
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<pre style="margin: 0;"> <span id="LC98" 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>
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<pre style="margin: 0;"> <span id="LC99" 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>
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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;"><span class="idiff left right">out</span>file</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="LC100" 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;"><span class="idiff left right">cov</span>file</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="LC101" 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="LC102" class="line" lang="cpp"></span>
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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>
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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>
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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>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// CNVs</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" 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;">CNV</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cnvs</span><span class="p">;</span></span>
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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="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;">hasGenoFile</span><span class="p">)</span> <span class="n" style="color: #333;">parseVcfCNV</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="n" style="color: #333;">cnvs</span><span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SVs for breakpoint refinement</span></span>
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108
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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="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;">SVBreakpoint</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TChrBreakpoints</span><span class="p">;</span></span>
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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="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;">TChrBreakpoints</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TGenomicBreakpoints</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">TGenomicBreakpoints</span> <span class="n" style="color: #333;">svbp</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;">TChrBreakpoints</span><span class="p">());</span></span>
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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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasVcfFile</span><span class="p">)</span> <span class="p">{</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" 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;">StructuralVariantRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">svs</span><span class="p">;</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">vcfParse</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="n" style="color: #333;">svs</span><span class="p">);</span></span>
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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">
114
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<pre style="margin: 0;">+<span id="LC114" 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;">svs</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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<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 class="n" style="color: #333;">svbp</span><span class="p">[</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SVBreakpoint</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciposlow</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciposhigh</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mapq</span><span class="p">));</span></span>
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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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">svbp</span><span class="p">[</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr2</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SVBreakpoint</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svEnd</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciendlow</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">ciendhigh</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">mapq</span><span class="p">));</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="p">}</span></span>
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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">
118
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<pre style="margin: 0;">+<span id="LC118" 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;">svbp</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;">sort</span><span class="p">(</span><span class="n" style="color: #333;">svbp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">svbp</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="p">(),</span> <span class="n" style="color: #333;">SortSVBreakpoint</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SVBreakpoint</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="p">}</span></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="c1" style="color: #998; font-style: italic;">// Iterate chromosomes</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">@@ -215,10 +234,21 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC234" 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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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// CNV discovery</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasGenoFile</span><span class="p">)</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;">// Call CNVs</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="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CNV</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">chrcnv</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">callCNVs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">gcbound</span><span class="p">,</span> <span class="n" style="color: #333;">gcContent</span><span class="p">,</span> <span class="n" style="color: #333;">uniqContent</span><span class="p">,</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">cov</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="n" style="color: #333;">chrcnv</span><span class="p">);</span></span>
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218
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="cpp"><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// Call CNVs</span></span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="cpp"><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//callCNVs(c, gcbound, gcContent, uniqContent, gcbias, cov, hdr, refIndex</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// Merge adjacent CNVs lacking read-depth shift</span></span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">mergeCNVs</span></span><span class="p"><span class="idiff">(</span></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">chrcnv</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cnvs</span></span><span class="p">);</span></span>
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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 class="c1" style="color: #998; font-style: italic;">// Refine breakpoints</span></span>
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247
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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;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasVcfFile</span><span class="p">)</span> <span class="n" style="color: #333;">breakpointRefinement</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">gcbound</span><span class="p">,</span> <span class="n" style="color: #333;">gcContent</span><span class="p">,</span> <span class="n" style="color: #333;">uniqContent</span><span class="p">,</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">cov</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="n" style="color: #333;">svbp</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</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>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> </span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// CNV genotyping</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">genotypeCNVs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">gcbound</span><span class="p">,</span> <span class="n" style="color: #333;">gcContent</span><span class="p">,</span> <span class="n" style="color: #333;">uniqContent</span><span class="p">,</span> <span class="n" style="color: #333;">gcbias</span><span class="p">,</span> <span class="n" style="color: #333;">cov</span><span class="p">,</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">refIndex</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</span><span class="p">);</span></span>
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"></span>
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// BED File (target intervals)</span></span>
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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>
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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">@@ -259,7 +289,8 @@ namespace torali</td>
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259
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289
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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;">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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260
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<pre style="margin: 0;"> <span id="LC290" 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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261
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291
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<pre style="margin: 0;"> <span id="LC291" 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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262
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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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292
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<pre style="margin: 0;">+<span id="LC292" 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="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 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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263
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294
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<pre style="margin: 0;"> <span id="LC294" 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="LC295" 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="LC296" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="345" style="width: 35px; color: rgba(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">@@ -314,7 +345,8 @@ namespace torali</td>
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314
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345
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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="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="LC346" 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="LC347" 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="LC348" 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="p">;</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 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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318
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<pre style="margin: 0;"> <span id="LC350" 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="LC351" 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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352
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<pre style="margin: 0;"> <span id="LC352" 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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<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 +372,8 @@ namespace torali</td>
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372
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<pre style="margin: 0;"> <span id="LC372" 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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373
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<pre style="margin: 0;"> <span id="LC373" 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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374
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<pre style="margin: 0;"> <span id="LC374" 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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343
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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>
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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;">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="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 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="LC377" 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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345
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reset</span></span>
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346
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379
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<pre style="margin: 0;"> <span id="LC379" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -387,63 +420,22 @@ namespace torali</td>
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387
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420
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<pre style="margin: 0;"> <span id="LC420" 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>
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388
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421
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<pre style="margin: 0;"> <span id="LC421" 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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389
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422
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<pre style="margin: 0;"> <span id="LC422" 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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390
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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>
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<pre style="margin: 0;">+<span id="LC423" 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="p">;</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 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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391
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425
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<pre style="margin: 0;"> <span id="LC425" 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="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="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="cpp"></span>
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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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398
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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>
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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>
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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>
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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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<pre style="margin: 0;">-<span id="LC403" class="line" lang="cpp"> <span class="p">{</span></span>
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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>
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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>
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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>
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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>
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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>
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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>
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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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412
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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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<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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<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>
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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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<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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429
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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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<pre style="margin: 0;">-<span id="LC432" class="line" lang="cpp"> <span class="p">}</span></span>
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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>
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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>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="cpp"> <span class="p">}</span></span>
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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>
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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>
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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>
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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>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Sort CNVs</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">cnvs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">cnvs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">SortCNVs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CNV</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Genotype CNVs</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">cnvVCF</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">cnvs</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC439" 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="LC440" 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="LC441" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -452,10 +444,6 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC444" 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="LC445" 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>
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<pre style="margin: 0;"> <span id="LC446" 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>
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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>
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<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>
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<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>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC448" 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>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"> <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">@@ -472,21 +460,30 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC460" 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>
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<pre style="margin: 0;"> <span id="LC461" 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>
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<pre style="margin: 0;"> <span id="LC462" 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>
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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>
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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>
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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>
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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>
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<pre style="margin: 0;">+<span id="LC463" 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;">cnvfile</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;">"cnv.bcf"</span><span class="p">),</span> <span class="s" style="color: #d14;">"output CNV file"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"covfile,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="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;">covfile</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;">"cov.gz"</span><span class="p">),</span> <span class="s" style="color: #d14;">"output coverage file"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="cpp"></span>
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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>
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<pre style="margin: 0;">+<span id="LC467" 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;">cnv</span><span class="p">(</span><span class="s" style="color: #d14;">"CNV calling"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">cnv</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="LC469" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"sdrd,x"</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;">stringency</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. SD read-depth shift"</span><span class="p">)</span></span>
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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;">"cn-offset,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;">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;">cn_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="mf" style="color: #099;">0.1</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. CN offset"</span><span class="p">)</span></span>
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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;">"cnv-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;">minCnvSize</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;">"min. CNV size"</span><span class="p">)</span></span>
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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;">"svfile,l"</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;">vcffile</span><span class="p">),</span> <span class="s" style="color: #d14;">"delly SV file for breakpoint refinement"</span><span class="p">)</span></span>
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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;">"vcffile,v"</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;">genofile</span><span class="p">),</span> <span class="s" style="color: #d14;">"input VCF/BCF file for re-genotyping"</span><span class="p">)</span></span>
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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;">"segmentation,u"</span><span class="p">,</span> <span class="s" style="color: #d14;">"copy-number segmentation"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC477" 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;">"Read-depth windows"</span><span class="p">);</span></span>
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478
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<pre style="margin: 0;"> <span id="LC478" 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>
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479
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<pre style="margin: 0;"> <span id="LC479" 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>
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484
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480
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<pre style="margin: 0;"> <span id="LC480" 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>
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485
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481
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<pre style="margin: 0;"> <span id="LC481" 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>
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486
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482
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<pre style="margin: 0;"> <span id="LC482" 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>
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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;">"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>
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487
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> <span class="p">;</span></span>
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488
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485
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="cpp"></span>
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489
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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 <span class="idiff left right">options</span>"</span><span class="p">);</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" 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 <span class="idiff left right">fragment normalization</span>"</span><span class="p">);</span></span>
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490
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487
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<pre style="margin: 0;"> <span id="LC487" 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>
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491
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488
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<pre style="margin: 0;"> <span id="LC488" 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>
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492
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489
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<pre style="margin: 0;"> <span id="LC489" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="499" style="width: 35px; color: rgba(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="496" style="width: 35px; color: rgba(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">@@ -499,7 +496,8 @@ namespace torali</td>
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499
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496
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<pre style="margin: 0;"> <span id="LC496" 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>
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500
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<td class="diff-line-num new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
497
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<pre style="margin: 0;"> <span id="LC497" 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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501
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498
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<pre style="margin: 0;"> <span id="LC498" 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>
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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>
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499
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<pre style="margin: 0;">+<span id="LC499" 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>
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<pre style="margin: 0;">+<span id="LC500" 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>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC503" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -507,9 +505,9 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set the visibility</span></span>
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507
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<pre style="margin: 0;"> <span id="LC507" 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>
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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>
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<pre style="margin: 0;">+<span id="LC508" 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;"><span class="idiff left">cnv</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff right">(</span></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>
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511
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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;">visible_options</span><span class="p">;</span></span>
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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>
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<pre style="margin: 0;">+<span id="LC510" 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;"><span class="idiff left">cnv</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff right">(</span></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>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse command-line</span></span>
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<pre style="margin: 0;"> <span id="LC513" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="551" style="width: 35px; color: rgba(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="549" style="width: 35px; color: rgba(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">@@ -551,15 +549,57 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC549" 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>
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<pre style="margin: 0;"> <span id="LC550" 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>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">CNV mode</span></span></span>
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<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;">"<span class="idiff left">panelfile"</span></span><span class="p"><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">hasPanelFile</span></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="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;"><span class="idiff left right">hasPanelFile</span></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="LC557" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">Segmentation</span></span></span>
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<pre style="margin: 0;">+<span id="LC553" 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;">"<span class="idiff left">segmentation"</span></span><span class="p"><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">segmentation</span></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="LC554" 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;"><span class="idiff left right">segmentation</span></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="LC555" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check window size</span></span>
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<pre style="margin: 0;"> <span id="LC557" 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>
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<pre style="margin: 0;"> <span id="LC558" 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>
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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="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>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check input VCF file (CNV genotyping)</span></span>
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<pre style="margin: 0;">+<span id="LC562" 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;">"vcffile"</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC563" 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;">genofile</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;">genofile</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;">genofile</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC564" 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;">"Input VCF/BCF 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;">genofile</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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565
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<pre style="margin: 0;">+<span id="LC565" 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>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="p">}</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ifile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">genofile</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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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ifile</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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569
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<pre style="margin: 0;">+<span id="LC569" 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;">genofile</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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570
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<pre style="margin: 0;">+<span id="LC570" 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>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="p">}</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" 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>
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574
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<pre style="margin: 0;">+<span id="LC574" 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 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;">genofile</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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575
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<pre style="margin: 0;">+<span id="LC575" 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>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="p">}</span></span>
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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;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_close</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasGenoFile</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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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"> <span class="p">}</span> <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;">hasGenoFile</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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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check input VCF file (delly SV file)</span></span>
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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;">vm</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"svfile"</span><span class="p">))</span> <span class="p">{</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" 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;">vcffile</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;">vcffile</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;">vcffile</span><span class="p">)))</span> <span class="p">{</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" 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;">"Input VCF/BCF 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;">vcffile</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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586
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<pre style="margin: 0;">+<span id="LC586" 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>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="p">}</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ifile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">vcffile</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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589
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<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;">ifile</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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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 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;">vcffile</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>
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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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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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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="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>
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595
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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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Fail to open index 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;">vcffile</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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596
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<pre style="margin: 0;">+<span id="LC596" 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>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="p">}</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_close</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasVcfFile</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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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="p">}</span> <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;">hasVcfFile</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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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> </span>
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563
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check bam file</span></span>
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564
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604
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<pre style="margin: 0;"> <span id="LC604" 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>
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565
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605
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<pre style="margin: 0;"> <span id="LC605" 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>
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<li id="5d775c4d26336d72c9aaeefa6f42a658ef123ac9">
<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#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">@@ -16,6 +16,7 @@</td>
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16
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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 "version.h"</span></span>
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17
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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 "delly.h"</span></span>
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18
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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 "filter.h"</span></span>
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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 "classify.h"</span></span>
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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 "merge.h"</span></span>
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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 "tegua.h"</span></span>
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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 "coral.h"</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">@@ -27,16 +28,17 @@ inline void</td>
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<pre style="margin: 0;"> <span id="LC28" 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="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;">"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="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 <span class="idiff left right">commands</span>:"</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;">"Short-read <span class="idiff left right">SV calling</span>:"</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;">" 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="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;">" 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>
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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="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>
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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="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="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 <span class="idiff left right">commands</span>:"</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="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;">"Long-read <span class="idiff left right">SV calling</span>:"</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="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="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="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="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="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>
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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>
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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;">"Copy-number variant calling:"</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="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="s" style="color: #d14;">" cnv discover and genotype copy-number 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="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="s" style="color: #d14;">" classify classify somatic or germline copy-number 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="LC42" 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="LC43" 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="LC44" class="line" lang="cpp"><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">@@ -73,9 +75,12 @@ int main(int argc, char **argv) {</td>
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<pre style="margin: 0;"> <span id="LC75" 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>
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<pre style="margin: 0;"> <span id="LC76" 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>
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75
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <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;">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;">"<span class="idiff left right">rd</span>"</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="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;">"<span class="idiff left right">cnv</span>"</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC79" 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>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="p">}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" 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;">"classify"</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">classify</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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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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79
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84
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<pre style="margin: 0;"> <span id="LC84" 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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85
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<pre style="margin: 0;"> <span id="LC85" 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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81
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#959a235a0b48a27af0667cc50c53360de917157d"><strong>src/delly.h</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">@@ -50,6 +50,7 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Config arguments</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">Config</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">islr</span><span class="p">;</span></span>
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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;">minMapQual</span><span class="p">;</span></span>
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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;">minTraQual</span><span class="p">;</span></span>
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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;">minGenoQual</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="201" style="width: 35px; color: rgba(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">@@ -200,7 +201,8 @@ namespace torali</td>
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200
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201
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<pre style="margin: 0;"> <span id="LC201" 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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201
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202
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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;">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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202
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203
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<pre style="margin: 0;"> <span id="LC203" 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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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">islr</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="LC205" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC206" 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="LC207" 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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<pre style="margin: 0;"> <span id="LC208" 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>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#836bf99511b7d355c156c4bd68f24fd0b7ce69c9"><strong>src/genotype.h</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">@@ -31,11 +31,71 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">Geno</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">svStartPrefix</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">svStartSuffix</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">svEndPrefix</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">svEndSuffix</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">svStart</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">svEnd</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">svt</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="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="p">};</span></span>
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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="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC36" 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;">TSRStore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TJunctionMap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TReadCountMap</span><span class="p">></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"></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;">float</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">percentIdentity</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="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">splitpos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">window</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get window boundaries</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ws</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;">splitpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">window</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="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">we</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;">splitpos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">window</span><span class="p">,</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;">s1</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="LC41" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Find percent identity</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;">bool</span> <span class="n" style="color: #333;">varSeen</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="LC43" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">refSeen</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="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refpos</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="LC45" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">gapMM</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="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mm</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="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">ma</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="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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">leftPerc</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>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">rightPerc</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>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">inGap</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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51
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<pre style="margin: 0;">+<span id="LC51" 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;">j</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;">j</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 class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">varSeen</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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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">[</span><span class="n" style="color: #333;">j</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>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">refSeen</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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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">refpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">splitpos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">refpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ws</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">refpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">we</span><span class="p">))</span> <span class="p">{</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">refpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">splitpos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">leftPerc</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="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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mm</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;">leftPerc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="p">}</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">refpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">we</span><span class="p">)</span> <span class="p">{</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">rightPerc</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="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mm</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;">rightPerc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="p">}</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">mm</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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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">ma</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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">gapMM</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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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="p">}</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">refpos</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="p">}</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">refSeen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">varSeen</span><span class="p">))</span> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Internal gap?</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">s2</span><span class="p">[</span><span class="n" style="color: #333;">j</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="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;">j</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>
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73
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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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">inGap</span><span class="p">)</span> <span class="p">{</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">inGap</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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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">gapMM</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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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">gapMM</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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78
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<pre style="margin: 0;">+<span id="LC78" 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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79
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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="n" style="color: #333;">inGap</span><span class="p">)</span> <span class="p">{</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gapMM</span><span class="p">;</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">inGap</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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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">}</span></span>
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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;">s2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</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;">j</span><span class="p">])</span> <span class="n" style="color: #333;">ma</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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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">mm</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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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="p">}</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="p">}</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="p">}</span></span>
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88
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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;">rightPerc</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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">rightPerc</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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90
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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;">ma</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mm</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;">rightPerc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mm</span><span class="p">);</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="p">}</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << ws << ',' << splitpos << ',' << we << ',' << leftPerc << ',' << rightPerc << std::endl;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" 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;">min</span><span class="p">(</span><span class="n" style="color: #333;">leftPerc</span><span class="p">,</span> <span class="n" style="color: #333;">rightPerc</span><span class="p">);</span> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="p">}</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC96" 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;">TJunctionMap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TReadCountMap</span><span class="p">></span></span>
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37
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97
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<pre style="margin: 0;"> <span id="LC97" 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="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">trackRef</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</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;">StructuralVariantRecord</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;">T<span class="idiff left">SRStore</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">srStore</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">T</span>JunctionMap</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;">TReadCountMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">covMap</span><span class="p">)</span> <span class="p">{</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">trackRef</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</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;">StructuralVariantRecord</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;">TJunctionMap</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;">TReadCountMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">covMap</span><span class="p">)</span> <span class="p">{</span></span>
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39
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99
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<pre style="margin: 0;"> <span id="LC99" 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;">StructuralVariantRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSVs</span><span class="p">;</span></span>
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40
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100
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<pre style="margin: 0;"> <span id="LC100" 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;">uint8_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TQuality</span><span class="p">;</span></span>
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41
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101
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<pre style="margin: 0;"> <span id="LC101" 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;">multi_array</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TAlign</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">@@ -113,7 +173,8 @@ namespace torali</td>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate all structural variants</span></span>
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<pre style="margin: 0;"> <span id="LC174" 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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115
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175
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<pre style="margin: 0;"> <span id="LC175" 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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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" 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;">svt</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="p">(</span><span class="n" style="color: #333;">itSV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> </span>
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117
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Lazy loading of reference sequence</span></span>
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118
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179
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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;">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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119
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<pre style="margin: 0;"> <span id="LC180" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="173" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -173,14 +234,14 @@ namespace torali</td>
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173
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << "svid:" << itSV->id << ",consensus-to-reference-alignment" << std::endl;</span></span>
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174
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t i = 0; i<align.shape()[0]; ++i) {</span></span>
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175
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (i == 0) {</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>int32_t cpos = 0;</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>for(uint32_t j = 0; j<align.shape()[1]; ++j) {</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>if (align[i][j] != '-') ++cpos;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>if (cpos == ad.cStart) std::cerr << '|';</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>else if (cpos == ad.cEnd) std::cerr << '|';</span></span>
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<td class="diff-line-num old old_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>else std::cerr << '#';</span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>}</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>std::cerr << std::endl;</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//int32_t cpos = 0;</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t j = 0; j<align.shape()[1]; ++j) {</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (align[i][j] != '-') ++cpos;</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (cpos == ad.cStart) std::cerr << '|';</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//else if (cpos == ad.cEnd) std::cerr << '|';</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//else std::cerr << '#';</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << std::endl;</span></span>
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184
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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185
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for(uint32_t j = 0; j<align.shape()[1]; ++j) std::cerr << align[i][j];</span></span>
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186
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247
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<pre style="margin: 0;"> <span id="LC247" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -265,18 +326,6 @@ namespace torali</td>
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265
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326
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<pre style="margin: 0;"> <span id="LC326" 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;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">TRefSeq</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSVSeqHit</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">TSVSeqHit</span> <span class="n" style="color: #333;">genoMap</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Any direct SV support</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" 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="LC270" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::size_t seed = hash_lr(rec);</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (srStore.find(seed) != srStore.end()) {</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for(uint32_t ri = 0; ri < srStore[seed].size(); ++ri) {</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> int32_t svid = srStore[seed][ri].svid;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (gbp[svid].left) genoMap.insert(std::make_pair(srStore[seed][ri].svid, srStore[seed][ri].sstart));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="275" 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="LC275" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> else genoMap.insert(std::make_pair(srStore[seed][ri].svid, srStore[seed][ri].sstart + srStore[seed][ri].inslen));</span></span>
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<pre style="margin: 0;">-<span id="LC276" 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="LC277" 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="LC278" 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="LC279" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse the CIGAR</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;">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="LC331" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -541,6 +590,280 @@ namespace torali</td>
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590
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<pre style="margin: 0;"> <span id="LC590" 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 class="n" style="color: #333;">file_c</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="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="cpp"> <span class="p">}</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"></span>
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594
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<pre style="margin: 0;">+<span id="LC594" 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;">TSRStore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TJunctionMap</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TReadCountMap</span><span class="p">></span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="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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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">genotypeLR</span><span class="p">(</span><span class="n" style="color: #333;">TConfig</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;">StructuralVariantRecord</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;">TSRStore</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">srStore</span><span class="p">,</span> <span class="n" style="color: #333;">TJunctionMap</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;">TReadCountMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">covMap</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC597" 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;">StructuralVariantRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSVs</span><span class="p">;</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"> </span>
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600
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<pre style="margin: 0;">+<span id="LC600" 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;">TMaxCoverage</span><span class="p">;</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" 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;">TMaxCoverage</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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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> </span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open file handles</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" 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;">samFile</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">TSamFile</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" 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;">hts_idx_t</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">TIndex</span><span class="p">;</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" 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;">bam_hdr_t</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">THeader</span><span class="p">;</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="n" style="color: #333;">TSamFile</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;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndex</span> <span class="n" style="color: #333;">idx</span><span class="p">(</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="n" style="color: #333;">size</span><span class="p">());</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="n" style="color: #333;">THeader</span> <span class="n" style="color: #333;">hdr</span><span class="p">(</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="n" style="color: #333;">size</span><span class="p">());</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">totalTarget</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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611
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<pre style="margin: 0;">+<span id="LC611" 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;">file_c</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;">file_c</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="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">file_c</span><span class="p">)</span> <span class="p">{</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="n" style="color: #333;">samfile</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="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;">files</span><span class="p">[</span><span class="n" style="color: #333;">file_c</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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613
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<pre style="margin: 0;">+<span id="LC613" 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;">file_c</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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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="n" style="color: #333;">idx</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="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;">file_c</span><span class="p">],</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="n" style="color: #333;">file_c</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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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">hdr</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="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 class="n" style="color: #333;">file_c</span><span class="p">]);</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="n" style="color: #333;">totalTarget</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;">file_c</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>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="p">}</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse genome chr-by-chr</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" 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="LC621" 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;">"SV annotation"</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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622
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<pre style="margin: 0;">+<span id="LC622" 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="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>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Ref aligned reads</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" 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;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TRefAlignCount</span><span class="p">;</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" 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;">TRefAlignCount</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TFileRefAlignCount</span><span class="p">;</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">TFileRefAlignCount</span> <span class="n" style="color: #333;">refAlignedReadCount</span><span class="p">(</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="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">TRefAlignCount</span><span class="p">());</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_c</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;">file_c</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="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">file_c</span><span class="p">)</span> <span class="n" style="color: #333;">refAlignedReadCount</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Dump file</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" 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;">dumpOut</span><span class="p">;</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" 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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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">dumpOut</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>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="n" style="color: #333;">dumpOut</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;">dumpfile</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="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">dumpOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"#svid</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bam</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">qname</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">matechr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">matepos</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">mapq</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">type"</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="LC636" class="line" lang="cpp"> <span class="p">}</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC639" 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;">fai</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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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate chromosomes</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" 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="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="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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642
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<pre style="margin: 0;">+<span id="LC642" 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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643
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<pre style="margin: 0;">+<span id="LC643" 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="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate samples</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_c</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;">file_c</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="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">file_c</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC647" 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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648
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<pre style="margin: 0;">+<span id="LC648" 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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649
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<pre style="margin: 0;">+<span id="LC649" 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>
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650
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<pre style="margin: 0;">+<span id="LC650" 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;">files</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">].</span><span class="n" style="color: #333;">string</span><span class="p">());</span></span>
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651
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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;">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="n" style="color: #333;">nodata</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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652
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<pre style="margin: 0;">+<span id="LC652" 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>
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653
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<pre style="margin: 0;">+<span id="LC653" 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>
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654
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<pre style="margin: 0;">+<span id="LC654" 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;">file_c</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>
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655
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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;">mapped</span><span class="p">)</span> <span class="n" style="color: #333;">nodata</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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656
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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;">nodata</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Flag breakpoints</span></span>
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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;">set</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;">TIdSet</span><span class="p">;</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" 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;">map</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="n" style="color: #333;">TIdSet</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TBpToIdMap</span><span class="p">;</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">TBpToIdMap</span> <span class="n" style="color: #333;">bpid</span><span class="p">;</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" 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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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="n" style="color: #333;">TBitSet</span> <span class="n" style="color: #333;">bpOccupied</span><span class="p">(</span><span class="n" style="color: #333;">hdr</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="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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664
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<pre style="margin: 0;">+<span id="LC664" 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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665
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<pre style="margin: 0;">+<span id="LC665" 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="p">{</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">bpOccupied</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;">svStart</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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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpid</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">svStart</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bpid</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="n" style="color: #333;">bpid</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;">itSV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">svStart</span><span class="p">,</span> <span class="n" style="color: #333;">TIdSet</span><span class="p">()));</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">bpid</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;">svStart</span><span class="p">].</span><span class="n" style="color: #333;">insert</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;">id</span><span class="p">);</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="p">}</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" 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;">chr2</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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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="n" style="color: #333;">bpOccupied</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;">svEnd</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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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpid</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">svEnd</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bpid</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="n" style="color: #333;">bpid</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;">itSV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">svEnd</span><span class="p">,</span> <span class="n" style="color: #333;">TIdSet</span><span class="p">()));</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="n" style="color: #333;">bpid</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;">svEnd</span><span class="p">].</span><span class="n" style="color: #333;">insert</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;">id</span><span class="p">);</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="p">}</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;">bpid</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>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Lazy loading of reference sequence</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" 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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<pre style="margin: 0;">+<span id="LC680" 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>
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681
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<pre style="margin: 0;">+<span id="LC681" 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="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;">target_name</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="LC682" class="line" lang="cpp"> <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;">fai</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;">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;">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;">seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC685" 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="LC686" 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;">TMaxCoverage</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TBpCoverage</span><span class="p">;</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">TBpCoverage</span> <span class="n" style="color: #333;">covBases</span><span class="p">(</span><span class="n" style="color: #333;">hdr</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="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="LC688" class="line" lang="cpp"></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Count reads</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" 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;">file_c</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="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="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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691
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<pre style="margin: 0;">+<span id="LC691" 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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692
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<pre style="margin: 0;">+<span id="LC692" 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;">file_c</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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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Genotyping only primary alignments</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" 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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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> </span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read hash</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" 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_lr</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Reference and sequence pointer</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" 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="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="c1" style="color: #998; font-style: italic;">// reference pointer</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" 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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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get sequence</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" 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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705
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<pre style="margin: 0;">+<span id="LC705" 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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706
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<pre style="margin: 0;">+<span id="LC706" 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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707
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<pre style="margin: 0;">+<span id="LC707" 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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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> </span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Any REF support</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" 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;">refAlign</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" 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;">altAlign</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" 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;">hits</span><span class="p">;</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" 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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714
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<pre style="margin: 0;">+<span id="LC714" 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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715
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<pre style="margin: 0;">+<span id="LC715" 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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<td class="diff-line-num new new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Fetch reference alignments</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" 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;">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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<td class="diff-line-num new new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rp</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;">file_c</span><span class="p">]</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;">covBases</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;">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;">covBases</span><span class="p">[</span><span class="n" style="color: #333;">rp</span><span class="p">];</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="n" style="color: #333;">refAlign</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">rp</span><span class="p">];</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="cpp"> <span class="n" style="color: #333;">altAlign</span> <span class="o" style="font-weight: 600;">+=</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>
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<td class="diff-line-num new new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpOccupied</span><span class="p">[</span><span class="n" style="color: #333;">rp</span><span class="p">])</span> <span class="n" style="color: #333;">hits</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">);</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" 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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723
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<pre style="margin: 0;">+<span id="LC723" 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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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
725
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<pre style="margin: 0;">+<span id="LC725" 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="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_CREF_SKIP</span><span class="p">))</span> <span class="p">{</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" 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;">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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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"> <span class="n" style="color: #333;">refAlign</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">rp</span><span class="p">];</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="n" style="color: #333;">altAlign</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">;</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bpOccupied</span><span class="p">[</span><span class="n" style="color: #333;">rp</span><span class="p">])</span> <span class="n" style="color: #333;">hits</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">rp</span><span class="p">);</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" 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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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" 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>
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<td class="diff-line-num new new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
733
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<pre style="margin: 0;">+<span id="LC733" 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;">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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<td class="diff-line-num new new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="cpp"> <span class="n" style="color: #333;">refAlign</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">;</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="cpp"> <span class="n" style="color: #333;">altAlign</span> <span class="o" style="font-weight: 600;">+=</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>
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736
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<pre style="margin: 0;">+<span id="LC736" 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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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
738
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<pre style="margin: 0;">+<span id="LC738" 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>
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<td class="diff-line-num new new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
739
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<pre style="margin: 0;">+<span id="LC739" 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>
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<td class="diff-line-num new new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
740
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<pre style="margin: 0;">+<span id="LC740" 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>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Do nothing</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" 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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743
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<pre style="margin: 0;">+<span id="LC743" 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>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"> <span class="p">}</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"> <span class="p">}</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Any ALT support?</span></span>
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<td class="diff-line-num new new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"> <span class="n" style="color: #333;">TIdSet</span> <span class="n" style="color: #333;">altAssigned</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">srStore</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">srStore</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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<td class="diff-line-num new new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
750
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<pre style="margin: 0;">+<span id="LC750" 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;">ri</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;">ri</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">srStore</span><span class="p">[</span><span class="n" style="color: #333;">seed</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;">ri</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC751" 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;">srStore</span><span class="p">[</span><span class="n" style="color: #333;">seed</span><span class="p">][</span><span class="n" style="color: #333;">ri</span><span class="p">].</span><span class="n" style="color: #333;">svid</span><span class="p">;</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svid</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>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if ((svs[svid].svt == 2) || (svs[svid].svt == 4)) continue;</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"> <span class="n" style="color: #333;">altAssigned</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">svid</span><span class="p">);</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" 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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756
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<pre style="margin: 0;">+<span id="LC756" 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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<pre style="margin: 0;">+<span id="LC757" 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;">svidStr</span><span class="p">(</span><span class="n" style="color: #333;">_addID</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">svt</span><span class="p">));</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" 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;">padNumber</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="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="p">(</span><span class="n" style="color: #333;">svid</span><span class="p">);</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp"> <span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">(),</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">);</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="cpp"> <span class="n" style="color: #333;">svidStr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">padNumber</span><span class="p">;</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">dumpOut</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">svidStr</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="n" style="color: #333;">file_c</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="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;">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="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;">hdr</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="n" style="color: #333;">target_name</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 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;">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="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;">hdr</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="n" style="color: #333;">target_name</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;">mtid</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;">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="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="kt" style="color: #458; font-weight: 600;">int32_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="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;">SR"</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="LC762" class="line" lang="cpp"> <span class="p">}</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ToDo</span></span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//jctMap[file_c][svid].alt.push_back((uint8_t) std::min((uint32_t) score, (uint32_t) rec->core.qual));</span></span>
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<pre style="margin: 0;">+<span id="LC767" 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;">alt</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="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="mi" style="color: #099;">20</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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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hpptr</span><span class="p">)</span> <span class="p">{</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" 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;">true</span><span class="p">;</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux2i</span><span class="p">(</span><span class="n" style="color: #333;">hpptr</span><span class="p">);</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hap</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;">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;">alth1</span><span class="p">;</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" 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;">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;">alth2</span><span class="p">;</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="cpp"> <span class="p">}</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="cpp"> <span class="p">}</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"> <span class="p">}</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Any REF support</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hits</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>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="cpp"></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Sufficiently long flank mapping?</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">rp</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="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="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="cpp"></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate all spanned SVs</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" 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;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hits</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;">idx</span><span class="p">)</span> <span class="p">{</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << hits[idx] - rec->core.pos << ',' << rp - hits[idx] << std::endl;</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="cpp"> </span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Long enough flanking sequence</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hits</span><span class="p">[</span><span class="n" style="color: #333;">idx</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;">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="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rp</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hits</span><span class="p">[</span><span class="n" style="color: #333;">idx</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;">minimumFlankSize</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Confident mapping?</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">percentIdentity</span><span class="p">(</span><span class="n" style="color: #333;">refAlign</span><span class="p">,</span> <span class="n" style="color: #333;">altAlign</span><span class="p">,</span> <span class="n" style="color: #333;">hits</span><span class="p">[</span><span class="n" style="color: #333;">idx</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;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minRefSep</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="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">percid</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">30</span><span class="p">;</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">score</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>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> </span>
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796
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<pre style="margin: 0;">+<span id="LC796" 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;">TIdSet</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">its</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bpid</span><span class="p">[</span><span class="n" style="color: #333;">hits</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]].</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">its</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bpid</span><span class="p">[</span><span class="n" style="color: #333;">hits</span><span class="p">[</span><span class="n" style="color: #333;">idx</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;">its</span><span class="p">)</span> <span class="p">{</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">its</span><span class="p">;</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if ((svs[svid].svt == 2) || (svs[svid].svt == 4)) continue;</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">altAssigned</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">svid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">altAssigned</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> </span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << svs[svid].chr << ',' << svs[svid].svStart << ',' << svs[svid].chr2 << ',' << svs[svid].svEnd << std::endl;</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" 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;">refAlignedReadCount</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="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" 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 new new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
803
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<pre style="margin: 0;">+<span id="LC803" 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="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">score</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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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hpptr</span><span class="p">)</span> <span class="p">{</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="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;">true</span><span class="p">;</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux2i</span><span class="p">(</span><span class="n" style="color: #333;">hpptr</span><span class="p">);</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hap</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;">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;">refh1</span><span class="p">;</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" 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;">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;">refh2</span><span class="p">;</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="cpp"> <span class="p">}</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="cpp"> <span class="p">}</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="cpp"> <span class="p">}</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="cpp"> <span class="p">}</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="cpp"> <span class="p">}</span></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" 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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816
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<pre style="margin: 0;">+<span id="LC816" 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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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="cpp"> </span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Assign SV support</span></span>
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<td class="diff-line-num new new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
819
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<pre style="margin: 0;">+<span id="LC819" 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;">svs</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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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">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="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">halfSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</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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<td class="diff-line-num new new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">_translocation</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">4</span><span class="p">))</span> <span class="n" style="color: #333;">halfSize</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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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="cpp"></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Left region</span></span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">lstart</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfSize</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="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">lend</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">covbase</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="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="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;">lstart</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">lend</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</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="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="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="n" style="color: #333;">covbase</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">covBases</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">covMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">leftRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covbase</span><span class="p">;</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Actual SV</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">covbase</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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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">mstart</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">mend</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svEnd</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">_translocation</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">4</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">mstart</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">halfSize</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="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">mend</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfSize</span><span class="p">,</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="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="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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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="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;">mstart</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">mend</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</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="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="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="n" style="color: #333;">covbase</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">covBases</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="cpp"> <span class="n" style="color: #333;">covMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covbase</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Right region</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="cpp"> <span class="n" style="color: #333;">covbase</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="LC844" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">rstart</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svEnd</span><span class="p">;</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">rend</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">halfSize</span><span class="p">,</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="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="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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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">_translocation</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">4</span><span class="p">))</span> <span class="p">{</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="cpp"> <span class="n" style="color: #333;">rstart</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span><span class="p">;</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"> <span class="n" style="color: #333;">rend</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">halfSize</span><span class="p">,</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="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="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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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="cpp"> <span class="p">}</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" 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;">rstart</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">rend</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</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="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="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="n" style="color: #333;">covbase</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">covBases</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="cpp"> <span class="n" style="color: #333;">covMap</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">][</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">rightRC</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">covbase</span><span class="p">;</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="cpp"> <span class="p">}</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp"> <span class="p">}</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="cpp"> <span class="p">}</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" 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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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"> <span class="p">}</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="cpp"> <span class="n" style="color: #333;">fai_destroy</span><span class="p">(</span><span class="n" style="color: #333;">fai</span><span class="p">);</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="cpp"></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_c</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;">file_c</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="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">file_c</span><span class="p">)</span> <span class="p">{</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" 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 class="n" style="color: #333;">file_c</span><span class="p">]);</span> </span>
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863
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<pre style="margin: 0;">+<span id="LC863" 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 class="n" style="color: #333;">file_c</span><span class="p">]);</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" 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 class="n" style="color: #333;">file_c</span><span class="p">]);</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"> <span class="p">}</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"> <span class="p">}</span></span>
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="cpp"> </span>
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="cpp"><span class="p">}</span></span>
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<li id="32e45cc4e811e711ac7f53e87e90add0070af5a7">
<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#32e45cc4e811e711ac7f53e87e90add0070af5a7"><strong>src/junction.h</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">@@ -248,10 +248,10 @@ namespace torali</td>
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Same direction, opposing soft-clips</span></span>
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249
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249
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<pre style="margin: 0;"> <span id="LC249" 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;">second</span><span class="p">[</span><span class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">scleft</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="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">scleft</span><span class="p">)</span> <span class="p">{</span></span>
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250
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250
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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;">it</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;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">scleft</span><span class="p">)</span> <span class="p">{</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">5to3</span></span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">3to5</span></span></span>
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252
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">br</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="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SRBamRecord</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</span><span class="p">,</span> <span class="n" style="color: #333;">rst</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;">it</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;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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 class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</span><span class="p">),</span> <span class="n" style="color: #333;">qval</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="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="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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>
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<pre style="margin: 0;"> <span id="LC253" 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="LC254" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">3to5</span></span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">5to3</span></span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">br</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="mi" style="color: #099;">3</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SRBamRecord</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</span><span class="p">,</span> <span class="n" style="color: #333;">rst</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;">it</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;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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 class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</span><span class="p">),</span> <span class="n" style="color: #333;">qval</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="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="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <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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<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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -259,10 +259,10 @@ namespace torali</td>
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259
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Opposing direction, same soft-clips</span></span>
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260
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260
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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;">it</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;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">scleft</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="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">scleft</span><span class="p">)</span> <span class="p">{</span></span>
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261
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261
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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;">it</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;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">scleft</span><span class="p">)</span> <span class="p">{</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">3to3</span></span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">5to5</span></span></span>
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263
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">br</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="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SRBamRecord</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</span><span class="p">,</span> <span class="n" style="color: #333;">rst</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;">it</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;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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 class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</span><span class="p">),</span> <span class="n" style="color: #333;">qval</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="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="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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>
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<pre style="margin: 0;"> <span id="LC264" 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="LC265" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">5to5</span></span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">3to3</span></span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">br</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="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">SRBamRecord</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr2ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refidx</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 class="n" style="color: #333;">chr1ev</span><span class="p">].</span><span class="n" style="color: #333;">refpos</span><span class="p">,</span> <span class="n" style="color: #333;">rst</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;">it</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;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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 class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</span><span class="p">),</span> <span class="n" style="color: #333;">qval</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="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="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">seqpos</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>
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267
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="p">}</span></span>
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268
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268
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<pre style="margin: 0;"> <span id="LC268" 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="427" style="width: 35px; color: rgba(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="427" style="width: 35px; color: rgba(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">@@ -427,10 +427,10 @@ namespace torali</td>
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427
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> <span class="n" style="color: #333;">fetchSVs</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;">TReadBp</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readBp</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;">SRBamRecord</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">br</span><span class="p">)</span> <span class="p">{</span></span>
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428
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Extract BAM records</span></span>
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429
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429
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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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">svtcmd</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="mi" style="color: #099;">2</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()))</span> <span class="n" style="color: #333;">selectDeletions</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">readBp</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">);</span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>if ((!c.svtcmd) || (c.svtset.find(3) != c.svtset.end())) selectDuplications(c, readBp, br);</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>if ((!c.svtcmd) || (c.svtset.find(0) != c.svtset.end()) || (c.svtset.find(1) != c.svtset.end())) selectInversions(c, readBp, br);</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" 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;">svtcmd</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="mi" style="color: #099;">3</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()))</span> <span class="n" style="color: #333;">selectDuplications</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">readBp</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">);</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="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;">svtcmd</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">svtset</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</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="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()))</span> <span class="n" style="color: #333;">selectInversions</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">readBp</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">);</span></span>
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432
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432
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<pre style="margin: 0;"> <span id="LC432" 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;">svtcmd</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="mi" style="color: #099;">4</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()))</span> <span class="n" style="color: #333;">selectInsertions</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">readBp</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">);</span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>if ((!c.svtcmd) || (c.svtset.find(5) != c.svtset.end()) || (c.svtset.find(6) != c.svtset.end()) || (c.svtset.find(7) != c.svtset.end()) || (c.svtset.find(8) != c.svtset.end())) selectTranslocations(c, readBp, br);</span></span>
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<pre style="margin: 0;">+<span id="LC433" 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;">svtcmd</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="mi" style="color: #099;">5</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;">svtset</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="mi" style="color: #099;">6</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;">svtset</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="mi" style="color: #099;">7</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;">svtset</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="mi" style="color: #099;">8</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;">svtset</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()))</span> <span class="n" style="color: #333;">selectTranslocations</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">readBp</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC436" 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;">TValidRegions</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TSvtSRBamRecord</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">@@ -457,7 +457,7 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC458" 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="LC459" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//outputSRBamRecords(c, srBR);</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Cluster BAM records</span></span>
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<pre style="margin: 0;"> <span id="LC462" 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;">svt</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;">svt</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">srBR</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;">svt</span><span class="p">)</span> <span class="p">{</span></span>
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463
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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;">srBR</span><span class="p">[</span><span class="n" style="color: #333;">svt</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="491" style="width: 35px; color: rgba(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="491" style="width: 35px; color: rgba(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">@@ -491,12 +491,12 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC491" 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="LC492" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Header</span></span>
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<pre style="margin: 0;">-<span id="LC494" 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;">"chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">chr2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">svtype</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ct</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">inslen"</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="LC494" 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;">"<span class="idiff left">id</span></span><span class="se" style="color: #d14;"><span class="idiff right">\t</span></span><span class="s" style="color: #d14;">chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">chr2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">svtype</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ct</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">inslen"</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="LC495" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SVs</span></span>
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<pre style="margin: 0;"> <span id="LC497" 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;">svt</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;">svt</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;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</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="LC498" 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;">br</span><span class="p">[</span><span class="n" style="color: #333;">svt</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="LC499" 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="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;">br</span><span class="p">[</span><span class="n" style="color: #333;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</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;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pos</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;">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;">br</span><span class="p">[</span><span class="n" style="color: #333;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr2</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;">br</span><span class="p">[</span><span class="n" style="color: #333;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pos2</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;">_addID</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="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">_addOrientation</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="sc" style="color: #d14;">'\t'</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;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">inslen</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="LC499" 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="n" style="color: #333;"><span class="idiff left">br</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">svt</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">id</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="sc" style="color: #d14;"><span class="idiff">'\t'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">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;">br</span><span class="p">[</span><span class="n" style="color: #333;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</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;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pos</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;">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;">br</span><span class="p">[</span><span class="n" style="color: #333;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr2</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;">br</span><span class="p">[</span><span class="n" style="color: #333;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">pos2</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;">_addID</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="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">_addOrientation</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="sc" style="color: #d14;">'\t'</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;">svt</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">inslen</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="LC500" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clean-up</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">@@ -528,7 +528,7 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC528" 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;">file_c</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="LC529" 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="LC530" 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;">file_c</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="LC531" 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="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">BAM_FSECONDARY</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">BAM_FSUPPLEMENTARY</span></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="LC531" 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="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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532
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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="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_lr</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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533
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533
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<pre style="margin: 0;"> <span id="LC533" 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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534
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">seed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hm</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="n" style="color: #333;">hm</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;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">qname</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">@@ -578,18 +578,24 @@ namespace torali</td>
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578
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<pre style="margin: 0;"> <span id="LC578" 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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579
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="cpp"></span>
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580
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Header</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" 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;">"chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">chr2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">svtype</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ct</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">peSupport</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">srSupport"</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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581
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<pre style="margin: 0;">+<span id="LC581" 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;">"chr1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">chr2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">pos2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">svtype</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ct</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">peSupport</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">srSupport</span><span class="se" style="color: #d14;"><span class="idiff left">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">consensus</span>"</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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582
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"> </span>
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583
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SVs</span></span>
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584
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584
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<pre style="margin: 0;"> <span id="LC584" 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;">svs</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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585
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585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" 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="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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</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;">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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr2</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svEnd</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;">_addID</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">_addOrientation</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">peSupport</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">srSupport</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="LC586" 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="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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svStart</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;">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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">chr2</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">svEnd</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;">_addID</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">_addOrientation</span><span class="p">(</span><span class="n" style="color: #333;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</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="sc" style="color: #d14;">'\t'</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">peSupport</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;">svs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">srSupport</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;"><span class="idiff left">'\t'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">svs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">consensus</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">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="LC587" class="line" lang="cpp"> <span class="p">}</span></span>
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC589" 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="LC590" 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="LC591" 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="LC592" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC594" 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="LC595" 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="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">outputStructuralVariants</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;">StructuralVariantRecord</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;">svs</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC597" 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="mi" style="color: #099;">8</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;">outputStructuralVariants</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">svs</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="LC598" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#88ce703739571701e1144b45c8b9e7a2ef9dd1c1"><strong>src/merge.h</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">@@ -41,6 +41,7 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">MergeConfig</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;">bool</span> <span class="n" style="color: #333;">filterForPass</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;">bool</span> <span class="n" style="color: #333;">filterForPrecise</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">cnvMode</span><span class="p">;</span></span>
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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;">chunksize</span><span class="p">;</span></span>
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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;">svcounter</span><span class="p">;</span></span>
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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;">bpoffset</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">@@ -117,7 +118,10 @@ void _fillIntervalMap(MergeConfig const& c, TGenomeIntervals& iScore, TContigMap</td>
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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="c1" style="color: #998; font-style: italic;">// Correct SV type</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">recsvt</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>
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<pre style="margin: 0;">-<span id="LC120" 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_string</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;">"SVTYPE"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">svt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nsvt</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;">bcf_get_info_string</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;">"CT"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nct</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;">recsvt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_decodeOrientation</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;">ct</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>
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<pre style="margin: 0;">+<span id="LC121" 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_string</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;">"SVTYPE"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">svt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nsvt</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="LC122" 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_string</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;">"CT"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ct</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nct</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;">recsvt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_decodeOrientation</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;">ct</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>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">recsvt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_decodeOrientation</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="s" style="color: #d14;">"NA"</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>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="p">}</span></span>
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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;">recsvt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">svtin</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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122
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"></span>
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123
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Correct size?</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" style="width: 35px; color: rgba(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="187" style="width: 35px; color: rgba(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">@@ -183,9 +187,12 @@ void _fillIntervalMap(MergeConfig const& c, TGenomeIntervals& iScore, TContigMap</td>
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183
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187
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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;">rv</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;">rv</span><span class="p">);</span></span>
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184
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rr</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;">rr</span><span class="p">);</span></span>
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185
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gt</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;">gt</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">maxvaf</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;">vaf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">maxcov</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;">coverage</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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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;">recsvt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">9</span><span class="p">)</span> <span class="p">{</span></span>
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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;">maxvaf</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;">vaf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">maxcov</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;">coverage</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="p">}</span></span>
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187
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="p">}</span></span>
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188
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Store the interval</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << tid << ',' << svStart << ',' << svEnd << ',' << rec->qual << std::endl;</span></span>
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189
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">iScore</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">IntervalScore</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;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">));</span></span>
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190
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"> <span class="p">}</span></span>
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191
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198
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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;">svend</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;">svend</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="548" style="width: 35px; color: rgba(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="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -548,6 +555,216 @@ void _outputSelectedIntervals(MergeConfig& c, TGenomeIntervals const& iSelected,</td>
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548
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">outfile</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;">14</span><span class="p">);</span></span>
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549
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"><span class="p">}</span></span>
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550
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cpp"></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"></span>
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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;">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;">TGenomeIntervals</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TContigMap</span><span class="p">></span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_outputSelectedIntervalsCNVs</span><span class="p">(</span><span class="n" style="color: #333;">MergeConfig</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;">TGenomeIntervals</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">iSelected</span><span class="p">,</span> <span class="n" style="color: #333;">TContigMap</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cMap</span><span class="p">)</span> <span class="p">{</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" 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;">TGenomeIntervals</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">TIntervalScores</span><span class="p">;</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" 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;">TIntervalScores</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">value_type</span> <span class="n" style="color: #333;">IntervalScore</span><span class="p">;</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"></span>
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565
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<pre style="margin: 0;">+<span id="LC565" 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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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;">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;">"Filtering SVs"</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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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open output VCF file</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</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;">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;">"wb"</span><span class="p">);</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hdr_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_init</span><span class="p">(</span><span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write VCF header</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" 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;">gregorian</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">date</span> <span class="n" style="color: #333;">today</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">now</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">();</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" 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;">datestr</span><span class="p">(</span><span class="s" style="color: #d14;">"##fileDate="</span><span class="p">);</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">datestr</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;">gregorian</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_iso_string</span><span class="p">(</span><span class="n" style="color: #333;">today</span><span class="p">);</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">datestr</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##ALT=<ID=CNV,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">copy-number variants</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FILTER=<ID=LowQual,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Poor quality copy-number variant</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=CIEND,Number=2,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Confidence interval around END</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=CIPOS,Number=2,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Confidence interval around POS</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=END,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">End position of the copy-number variant</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=MP,Number=1,Type=Float,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Mappable fraction of CNV</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Imprecise copy-number variant</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SVTYPE,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type of structural variant</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"##INFO=<ID=SVMETHOD,Number=1,Type=String,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Type of approach used to detect CNV</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"> </span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add reference contigs</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">numseq</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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589
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<pre style="margin: 0;">+<span id="LC589" 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;">map</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="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;">TReverseMap</span><span class="p">;</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="n" style="color: #333;">TReverseMap</span> <span class="n" style="color: #333;">rMap</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
591
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<pre style="margin: 0;">+<span id="LC591" 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;">TContigMap</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">cIt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cMap</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">cIt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">cMap</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;">cIt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">numseq</span><span class="p">)</span> <span class="n" style="color: #333;">rMap</span><span class="p">[</span><span class="n" style="color: #333;">cIt</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;">cIt</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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<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="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;">TReverseMap</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">rIt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rMap</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">rIt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">rMap</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;">rIt</span><span class="p">)</span> <span class="p">{</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="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;">refname</span><span class="p">(</span><span class="s" style="color: #d14;">"##contig=<ID="</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="n" style="color: #333;">refname</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rIt</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="p">;</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">refname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="p">}</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_add_sample</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_hdr_write</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">hdr_out</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;">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;">"Error: Failed to write BCF header!"</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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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Duplicate filter (identical start, end, score values)</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" 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;">TStartEnd</span><span class="p">;</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" 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;">TStartEnd</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TIntervalSet</span><span class="p">;</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" 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;">TIntervalSet</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TGenomicIntervalSet</span><span class="p">;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"> <span class="n" style="color: #333;">TGenomicIntervalSet</span> <span class="n" style="color: #333;">gis</span><span class="p">(</span><span class="n" style="color: #333;">numseq</span><span class="p">);</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse input VCF files</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_init</span><span class="p">();</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" 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;">htsFile</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">THtsFile</span><span class="p">;</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" 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;">bcf_hdr_t</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">TBcfHeader</span><span class="p">;</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" 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;">bcf1_t</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">TBcfRecord</span><span class="p">;</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" 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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TEof</span><span class="p">;</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="n" style="color: #333;">THtsFile</span> <span class="n" style="color: #333;">ifile</span><span class="p">(</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="n" style="color: #333;">size</span><span class="p">());</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"> <span class="n" style="color: #333;">TBcfHeader</span> <span class="n" style="color: #333;">hdr</span><span class="p">(</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="n" style="color: #333;">size</span><span class="p">());</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="n" style="color: #333;">TBcfRecord</span> <span class="n" style="color: #333;">rec</span><span class="p">(</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="n" style="color: #333;">size</span><span class="p">());</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">TEof</span> <span class="n" style="color: #333;">eof</span><span class="p">(</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="n" style="color: #333;">size</span><span class="p">());</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">allEOF</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="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
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<pre style="margin: 0;">+<span id="LC617" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_c</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;">file_c</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="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">file_c</span><span class="p">)</span> <span class="p">{</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">ifile</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="n" style="color: #333;">bcf_open</span><span class="p">(</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="n" style="color: #333;">file_c</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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<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
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="n" style="color: #333;">hdr</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="n" style="color: #333;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]);</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_hdr_set_samples</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</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;">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;">"Error: Failed to set sample information!"</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="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
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">rec</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="n" style="color: #333;">bcf_init</span><span class="p">();</span></span>
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<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
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">],</span> <span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">],</span> <span class="n" style="color: #333;">rec</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;">0</span><span class="p">)</span> <span class="p">{</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_unpack</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">],</span> <span class="n" style="color: #333;">BCF_UN_INFO</span><span class="p">);</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">eof</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="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" 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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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">allEOF</span><span class="p">;</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">eof</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="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="p">}</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="p">}</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"></span>
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<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="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nsvend</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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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <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;">svend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nmp</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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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nsvt</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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636
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<pre style="margin: 0;">+<span id="LC636" 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;">svt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ncipos</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="LC638" class="line" lang="cpp"> <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;">cipos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">nciend</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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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp"> <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;">ciend</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">allEOF</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="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Find next sorted record</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">idx</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>
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<pre style="margin: 0;">+<span id="LC644" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_c</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;">file_c</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="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">file_c</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC645" 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;">eof</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">])</span> <span class="p">{</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="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="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;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rid</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rid</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="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rid</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="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</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;">rec</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="n" style="color: #333;">pos</span><span class="p">)))</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_c</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"> <span class="p">}</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp"> <span class="p">}</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp"></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Correct SV type</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">recsvt</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>
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<pre style="margin: 0;">+<span id="LC652" 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_string</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;">"SVTYPE"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">svt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nsvt</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;">recsvt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_decodeOrientation</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="s" style="color: #d14;">"NA"</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>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// CNV ?</span></span>
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<pre style="margin: 0;">+<span id="LC654" 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;">9</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check PASS</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">pass</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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657
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<pre style="margin: 0;">+<span id="LC657" 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;">filterForPass</span><span class="p">)</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_has_filter</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="k" style="font-weight: 600;">const_cast</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="p">(</span><span class="s" style="color: #d14;">"PASS"</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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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="cpp"></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check PRECISE</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">precise</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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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">passPrecise</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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662
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<pre style="margin: 0;">+<span id="LC662" 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_flag</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;">"PRECISE"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="n" style="color: #333;">precise</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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663
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<pre style="margin: 0;">+<span id="LC663" 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;">filterForPrecise</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;">precise</span><span class="p">))</span> <span class="n" style="color: #333;">passPrecise</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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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check PASS and precise</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">passPrecise</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pass</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Correct size</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" 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="p">(</span><span class="n" style="color: #333;">bcf_hdr_id2name</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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rid</span><span class="p">));</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cMap</span><span class="p">[</span><span class="n" style="color: #333;">chrName</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</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>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="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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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse INFO fields</span></span>
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<pre style="margin: 0;">+<span id="LC675" 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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Is this a selected interval</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TIntervalScores</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">iter</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;">iSelected</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">iSelected</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">IntervalScore</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;">score</span><span class="p">),</span> <span class="n" style="color: #333;">SortIScores</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">IntervalScore</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">foundInterval</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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681
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<pre style="margin: 0;">+<span id="LC681" 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;">iter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">iSelected</span><span class="p">[</span><span class="n" style="color: #333;">tid</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;">iter</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;">svStart</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">iter</span><span class="p">)</span> <span class="p">{</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">iter</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;">svStart</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</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="p">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">score</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Duplicate?</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gis</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">find</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;">svStart</span><span class="p">,</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;">gis</span><span class="p">[</span><span class="n" style="color: #333;">tid</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="LC685" class="line" lang="cpp"> <span class="n" style="color: #333;">foundInterval</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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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">gis</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;">svStart</span><span class="p">,</span> <span class="n" style="color: #333;">svEnd</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="p">}</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="p">}</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">foundInterval</span><span class="p">)</span> <span class="p">{</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Fetch missing INFO fields</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <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;">"CIPOS"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cipos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ncipos</span><span class="p">);</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <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;">"CIEND"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ciend</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nciend</span><span class="p">);</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mpval</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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696
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<pre style="margin: 0;">+<span id="LC696" 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_float</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;">"MP"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</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;">nmp</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;">mpval</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mp</span><span class="p">;</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> </span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Create new record</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">rout</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_name2id</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</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>
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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;">rout</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;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</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>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="n" style="color: #333;">rout</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;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" 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;">files</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="n" style="color: #333;">id</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;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Within one VCF file IDs are unique</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="cpp"> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">_addID</span><span class="p">(</span><span class="n" style="color: #333;">recsvt</span><span class="p">);</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" 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;">padNumber</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="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="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">svcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="cpp"> <span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">padNumber</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">(),</span> <span class="sc" style="color: #d14;">'0'</span><span class="p">);</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">padNumber</span><span class="p">;</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"> <span class="p">}</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_id</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="n" style="color: #333;">id</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="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
711
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<pre style="margin: 0;">+<span id="LC711" 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;">refAllele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">allele</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" 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;">altAllele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">allele</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
713
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<pre style="margin: 0;">+<span id="LC713" 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;">alleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refAllele</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;">altAllele</span><span class="p">;</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_alleles_str</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="n" style="color: #333;">alleles</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="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">tmppass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_id2int</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_DT_ID</span><span class="p">,</span> <span class="s" style="color: #d14;">"PASS"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_filter</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tmppass</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> </span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add INFO fields</span></span>
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<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">precise</span><span class="p">)</span> <span class="n" style="color: #333;">bcf_update_info_flag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="s" style="color: #d14;">"PRECISE"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">bcf_update_info_flag</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="s" style="color: #d14;">"IMPRECISE"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_string</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">,</span> <span class="n" style="color: #333;">_addID</span><span class="p">(</span><span class="n" style="color: #333;">recsvt</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" 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;">dellyVersion</span><span class="p">(</span><span class="s" style="color: #d14;">"EMBL.DELLYv"</span><span class="p">);</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"> <span class="n" style="color: #333;">dellyVersion</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">dellyVersionNumber</span><span class="p">;</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_string</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span><span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="s" style="color: #d14;">"SVMETHOD"</span><span class="p">,</span> <span class="n" style="color: #333;">dellyVersion</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</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="mi" style="color: #099;">1</span><span class="p">);</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="s" style="color: #d14;">"CIPOS"</span><span class="p">,</span> <span class="n" style="color: #333;">cipos</span><span class="p">,</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="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_int32</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="s" style="color: #d14;">"CIEND"</span><span class="p">,</span> <span class="n" style="color: #333;">ciend</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_info_float</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">,</span> <span class="s" style="color: #d14;">"MP"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mpval</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write record</span></span>
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<td class="diff-line-num new new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_write1</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rout</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_clear1</span><span class="p">(</span><span class="n" style="color: #333;">rout</span><span class="p">);</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << bcf_hdr_id2name(hdr[idx], tid) << '\t' << svStart << '\t' << svEnd << std::endl;</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="cpp"> <span class="p">}</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="cpp"> <span class="p">}</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="cpp"> <span class="p">}</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="p">}</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Fetch next record</span></span>
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<td class="diff-line-num new new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bcf_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">[</span><span class="n" style="color: #333;">idx</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="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">bcf_unpack</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="n" style="color: #333;">BCF_UN_INFO</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">allEOF</span><span class="p">;</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">eof</span><span class="p">[</span><span class="n" style="color: #333;">idx</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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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"> <span class="p">}</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" 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="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;">svend</span><span class="p">);</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mp</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;">mp</span><span class="p">);</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" 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="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;">svt</span><span class="p">);</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cipos</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;">cipos</span><span class="p">);</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ciend</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;">ciend</span><span class="p">);</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="cpp"></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clean-up</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" 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;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_c</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;">file_c</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="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">file_c</span><span class="p">)</span> <span class="p">{</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]);</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_close</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]);</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="n" style="color: #333;">file_c</span><span class="p">]);</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"> <span class="p">}</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="cpp"></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Close VCF file</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">rout</span><span class="p">);</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr_out</span><span class="p">);</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Build index</span></span>
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<td class="diff-line-num new new_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">outfile</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;">14</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC768" 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="LC769" class="line" lang="cpp"><span class="n" style="color: #333;">mergeBCFs</span><span class="p">(</span><span class="n" style="color: #333;">MergeConfig</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;">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="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cts</span><span class="p">)</span> <span class="p">{</span></span>
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770
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<pre style="margin: 0;"> <span id="LC770" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="660" style="width: 35px; color: rgba(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="877" style="width: 35px; color: rgba(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">@@ -660,7 +877,8 @@ mergeRun(MergeConfig& c, int32_t const svt) {</td>
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660
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877
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<pre style="margin: 0;"> <span id="LC877" 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;">numseq</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;">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;">iSelected</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">iSelected</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="p">(),</span> <span class="n" style="color: #333;">SortIScores</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">IntervalScore</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="cpp"></span>
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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output best intervals</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp"> <span class="n" style="color: #333;">_outputSelectedIntervals</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">iSelected</span><span class="p">,</span> <span class="n" style="color: #333;">contigMap</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" 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;">9</span><span class="p">)</span> <span class="n" style="color: #333;">_outputSelectedIntervalsCNVs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">iSelected</span><span class="p">,</span> <span class="n" style="color: #333;">contigMap</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">_outputSelectedIntervals</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">iSelected</span><span class="p">,</span> <span class="n" style="color: #333;">contigMap</span><span class="p">,</span> <span class="n" style="color: #333;">svt</span><span class="p">);</span></span>
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="cpp"></span>
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// End</span></span>
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884
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<pre style="margin: 0;"> <span id="LC884" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="901" style="width: 35px; color: rgba(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">@@ -683,6 +901,7 @@ int merge(int argc, char **argv) {</td>
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683
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"coverage,v"</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;">coverage</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. coverage"</span><span class="p">)</span></span>
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684
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"minsize,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;">minsize</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;">0</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. SV size"</span><span class="p">)</span></span>
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685
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"maxsize,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;">maxsize</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;">1000000</span><span class="p">),</span> <span class="s" style="color: #d14;">"max. SV size"</span><span class="p">)</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"cnvmode,e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Merge delly CNV files"</span><span class="p">)</span></span>
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686
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905
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"precise,c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Filter sites for PRECISE"</span><span class="p">)</span></span>
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687
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906
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<pre style="margin: 0;"> <span id="LC906" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"pass,p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Filter sites for PASS"</span><span class="p">)</span></span>
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688
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="cpp"> <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">@@ -728,6 +947,14 @@ int merge(int argc, char **argv) {</td>
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728
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947
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<pre style="margin: 0;"> <span id="LC947" 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;">"precise"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">filterForPrecise</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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729
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948
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<pre style="margin: 0;"> <span id="LC948" 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;">filterForPrecise</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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730
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949
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<pre style="margin: 0;"> <span id="LC949" class="line" lang="cpp"></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Merge CNVs</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" 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;">"cnvmode"</span><span class="p">))</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">cnvMode</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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952
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<pre style="margin: 0;">+<span id="LC952" 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;">cnvMode</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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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check output files</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" 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;">_outfileValid</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="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" 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;">_outfileValid</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;">path</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;">string</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".csi"</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"></span>
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731
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Show cmd</span></span>
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959
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<pre style="margin: 0;"> <span id="LC959" 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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733
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960
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<pre style="margin: 0;"> <span id="LC960" 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>
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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">@@ -797,9 +1024,15 @@ int merge(int argc, char **argv) {</td>
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="cpp"> <span class="p">}</span></span>
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="cpp"> </span>
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1026
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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Run merging</span></span>
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">minSVT</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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1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">maxSVT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span><span class="p">;</span></span>
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1029
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<pre style="margin: 0;">+<span id="LC1029" 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;">cnvMode</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">minSVT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">9</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">maxSVT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"> <span class="p">}</span></span>
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1033
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<pre style="margin: 0;"> <span id="LC1033" 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;">oldPath</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>
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801
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<pre style="margin: 0;">-<span id="LC801" 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;">svtCollect</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">9</span></span><span class="p">);</span></span>
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802
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<pre style="margin: 0;">-<span id="LC802" 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;">svt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">svt</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">9</span></span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" 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;">svtCollect</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">maxSVT</span></span><span class="p">);</span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" 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;">svt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">minSVT</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">svt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxSVT</span></span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>
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803
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1036
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<pre style="margin: 0;"> <span id="LC1036" 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;">uuids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">uuid</span> <span class="n" style="color: #333;">uuid</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;">uuids</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">random_generator</span><span class="p">()();</span></span>
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804
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1037
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<pre style="margin: 0;"> <span id="LC1037" 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;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"svt"</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="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="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;">"_"</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="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="p">(</span><span class="n" style="color: #333;">uuid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".bcf"</span><span class="p">;</span></span>
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="cpp"> <span class="n" style="color: #333;">svtCollect</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="n" style="color: #333;">filename</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">@@ -843,10 +1076,19 @@ int merge(int argc, char **argv) {</td>
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Merge temporary files</span></span>
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1078
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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldPath</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="cpp"> <span class="n" style="color: #333;">mergeBCFs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">svtCollect</span><span class="p">);</span></span>
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847
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<pre style="margin: 0;">-<span id="LC847" 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;">svt</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;">svt</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">9</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</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="LC848" 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;">remove</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</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="LC849" 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;">remove</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;">path</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</span><span class="p">[</span><span class="n" style="color: #333;">svt</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="s" style="color: #d14;">".csi"</span><span class="p">));</span></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" 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;">cnvMode</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Copy</span></span>
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<pre style="margin: 0;">+<span id="LC1081" 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;">copy_file</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</span><span class="p">[</span><span class="mi" style="color: #099;">9</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>
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1082
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<pre style="margin: 0;">+<span id="LC1082" 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;">copy_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;">filesystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">path</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</span><span class="p">[</span><span class="mi" style="color: #099;">9</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="s" style="color: #d14;">".csi"</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;">path</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;">string</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".csi"</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Delete</span></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" 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;">remove</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]);</span></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" 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;">remove</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;">path</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</span><span class="p">[</span><span class="mi" style="color: #099;">9</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="s" style="color: #d14;">".csi"</span><span class="p">));</span></span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" 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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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"> <span class="n" style="color: #333;">mergeBCFs</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">svtCollect</span><span class="p">);</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" 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;">svt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minSVT</span><span class="p">;</span> <span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">maxSVT</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">svt</span><span class="p">)</span> <span class="p">{</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" 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;">remove</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</span><span class="p">[</span><span class="n" style="color: #333;">svt</span><span class="p">]);</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" 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;">remove</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;">path</span><span class="p">(</span><span class="n" style="color: #333;">svtCollect</span><span class="p">[</span><span class="n" style="color: #333;">svt</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="s" style="color: #d14;">".csi"</span><span class="p">));</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"> <span class="p">}</span></span>
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="cpp"> <span class="p">}</span></span>
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851
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1093
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<pre style="margin: 0;"> <span id="LC1093" 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>
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852
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1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="cpp"><span class="p">}</span></span>
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<li id="961fb7e93e491fbba61e895bde9438ca23a92e42">
<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#961fb7e93e491fbba61e895bde9438ca23a92e42"><strong>src/modvcf.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="453" style="width: 35px; color: rgba(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="453" style="width: 35px; color: rgba(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">@@ -453,7 +453,7 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord> const& svs, TJ</td>
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453
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<td class="diff-line-num new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=RC,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Raw high-quality read counts or base counts for the SV</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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454
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<td class="diff-line-num new_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=RCL,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Raw high-quality read counts or base counts for the left control region</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
455
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<td class="diff-line-num new_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=RCR,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Raw high-quality read counts or base counts for the right control region</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="456" 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">
456
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<td class="diff-line-num new_line old" data-linenumber="456" 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="LC456" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=CN,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Read-depth based copy-number estimate for autosomal sites</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=<span class="idiff left right">RD</span>CN,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">Read-depth based copy-number estimate for autosomal sites</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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457
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<td class="diff-line-num new_line" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=DR,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"># high-quality reference pairs</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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458
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_append</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"># high-quality variant pairs</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>"</span><span class="p">);</span></span>
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459
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459
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<pre style="margin: 0;"> <span id="LC459" 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;">isHaplotagged</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="665" style="width: 35px; color: rgba(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="665" style="width: 35px; color: rgba(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">@@ -665,7 +665,7 @@ vcfOutput(TConfig const& c, std::vector<TStructuralVariantRecord> const& svs, TJ</td>
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665
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"RCL"</span><span class="p">,</span> <span class="n" style="color: #333;">rcl</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>
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666
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666
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"RC"</span><span class="p">,</span> <span class="n" style="color: #333;">rc</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>
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"RCR"</span><span class="p">,</span> <span class="n" style="color: #333;">rcr</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>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"CN"</span><span class="p">,</span> <span class="n" style="color: #333;">cnest</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>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"<span class="idiff left right">RD</span>CN"</span><span class="p">,</span> <span class="n" style="color: #333;">cnest</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>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"DR"</span><span class="p">,</span> <span class="n" style="color: #333;">drcount</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>
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670
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670
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_update_format_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;">"DV"</span><span class="p">,</span> <span class="n" style="color: #333;">dvcount</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>
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<pre style="margin: 0;"> <span id="LC671" 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;">isHaplotagged</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#8f130c1406eeae226d6453bcf3ab844ecd2c707b"><strong>src/msa.h</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">@@ -288,6 +288,13 @@ namespace torali {</td>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">shape</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="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>
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<pre style="margin: 0;">+<span id="LC291" 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;">TStructuralVariant</span><span class="p">></span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="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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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">outputConsensus</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;">TStructuralVariant</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sv</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;">cons</span><span class="p">)</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;">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;">">"</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;">sv</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="sc" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">svStart</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;">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;">sv</span><span class="p">.</span><span class="n" style="color: #333;">chr2</span><span class="p">]</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;">sv</span><span class="p">.</span><span class="n" style="color: #333;">svEnd</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" SVT:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" SR:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">srSupport</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" PE:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">peSupport</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="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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cons</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="LC296" class="line" lang="cpp"> <span class="p">}</span></span>
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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="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="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#de10b670208808941807d0db7069159f2749af37"><strong>src/split.h</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">@@ -463,7 +463,7 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC463" 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;">finalGapStart</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="LC464" 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;">finalGapEnd</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="LC465" 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;">_coordTransform</span><span class="p">(</span><span class="n" style="color: #333;">svRefStr</span><span class="p">,</span> <span class="n" style="color: #333;">bp</span><span class="p">,</span> <span class="n" style="color: #333;">ad</span><span class="p">,</span> <span class="n" style="color: #333;">finalGapStart</span><span class="p">,</span> <span class="n" style="color: #333;">finalGapEnd</span><span class="p">,</span> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">svt</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>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">precise</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="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">svStart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">finalGapStart</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</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;">finalGapEnd</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">@@ -475,6 +475,32 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">ciposhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ci_wiggle</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">ciendlow</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ci_wiggle</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">ciendhigh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ci_wiggle</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC479" 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;">islr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Set alleles</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">alleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_addAlleles</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;">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;">sv</span><span class="p">.</span><span class="n" style="color: #333;">svStart</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;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">svStart</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;">sv</span><span class="p">.</span><span class="n" style="color: #333;">chr2</span><span class="p">]),</span> <span class="n" style="color: #333;">sv</span><span class="p">,</span> <span class="n" style="color: #333;">sv</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="LC482" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get exact alleles for INS and DEL </span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">sv</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="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">sv</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;">4</span><span class="p">))</span> <span class="p">{</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" 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;">refVCF</span><span class="p">;</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" 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;">altVCF</span><span class="p">;</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cpos</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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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">inSV</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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489
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<pre style="margin: 0;">+<span id="LC489" 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;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">align</span><span class="p">.</span><span class="n" style="color: #333;">shape</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="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">j</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>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cpos</span><span class="p">;</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ad</span><span class="p">.</span><span class="n" style="color: #333;">cStart</span><span class="p">)</span> <span class="n" style="color: #333;">inSV</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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493
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<pre style="margin: 0;">+<span id="LC493" 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;">cpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ad</span><span class="p">.</span><span class="n" style="color: #333;">cEnd</span><span class="p">)</span> <span class="n" style="color: #333;">inSV</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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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="p">}</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">inSV</span><span class="p">)</span> <span class="p">{</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">altVCF</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">align</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">j</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="n" style="color: #333;">refVCF</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">align</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="p">}</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="p">}</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="n" style="color: #333;">sv</span><span class="p">.</span><span class="n" style="color: #333;">alleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_addAlleles</span><span class="p">(</span><span class="n" style="color: #333;">refVCF</span><span class="p">,</span> <span class="n" style="color: #333;">altVCF</span><span class="p">);</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="p">}</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <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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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="p">}</span></span>
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#76bf896cda9e6b76c0af8350e53bb4bc92d6d281"><strong>src/tags.h</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">@@ -17,7 +17,7 @@ namespace torali {</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"></span>
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18
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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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19
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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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20
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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>
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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 class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">svt</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">9</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="p">}</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="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 unfold js-unfold old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -198,8 +198,21 @@ namespace torali {</td>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"></span>
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199
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<pre style="margin: 0;"> <span id="LC199" 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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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">_isizeMappingPos</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="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">isize</span><span class="p">)</span> <span class="p">{</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_translocation</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</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;">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>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_translocation</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">))</span> <span class="p">{</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">orient</span> <span class="o" style="font-weight: 600;">=</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>
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203
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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;">orient</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="n" style="color: #333;">DELLY_SVT_TRANS</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="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" 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;">orient</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="n" style="color: #333;">DELLY_SVT_TRANS</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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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <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="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 3to5 or 5to3?</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" 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;">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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" 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_FREVERSE</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DELLY_SVT_TRANS</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="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" 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;">DELLY_SVT_TRANS</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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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" 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="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" 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_FREVERSE</span><span class="p">))</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DELLY_SVT_TRANS</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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212
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<pre style="margin: 0;">+<span id="LC212" 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;">DELLY_SVT_TRANS</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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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="p">}</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" 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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203
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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
216
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<pre style="margin: 0;"> <span id="LC216" 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="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 class="c1" style="color: #998; font-style: italic;">// No SV</span></span>
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204
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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">orient</span> <span class="o" style="font-weight: 600;">=</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>
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205
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218
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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;">orient</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -211,7 +224,7 @@ namespace torali {</td>
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<td class="diff-line-num old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
211
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224
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">abs</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="mi" style="color: #099;">100</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 class="c1" style="color: #998; font-style: italic;">// Too small</span></span>
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212
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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213
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <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 class="idiff left right"> </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 class="p">}</span></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 class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">hash_string</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">s</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#0295016a39c777dffa48c5e5efc6af0fb6982a0a"><strong>src/tegua.h</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">@@ -34,8 +34,8 @@ namespace torali {</td>
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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>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">TeguaConfig</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">islr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasDumpFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" 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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<pre style="margin: 0;"> <span id="LC39" 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="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isHaplotagged</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;">bool</span> <span class="n" style="color: #333;">svtcmd</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">@@ -46,6 +46,7 @@ namespace torali {</td>
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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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<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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<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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<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;">maxReadPerSV</span><span class="p">;</span></span>
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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;">nchr</span><span class="p">;</span></span>
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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;">minimumFlankSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +55,6 @@ namespace torali {</td>
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<pre style="margin: 0;"> <span id="LC55" 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;">aliscore</span><span class="p">;</span></span>
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55
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56
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<pre style="margin: 0;"> <span id="LC56" 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;">dumpfile</span><span class="p">;</span></span>
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57
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<pre style="margin: 0;"> <span id="LC57" 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>
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<pre style="margin: 0;">-<span id="LC57" 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;">vcffile</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;"> <span id="LC58" 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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59
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<pre style="margin: 0;"> <span id="LC59" 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="LC60" 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;">exclude</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(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">@@ -106,20 +106,24 @@ namespace torali {</td>
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<pre style="margin: 0;"> <span id="LC106" 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>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Split-read assembly?</span></span>
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<pre style="margin: 0;">-<span id="LC110" 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;">hasVcfFile</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SR Store</span></span>
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<pre style="margin: 0;">+<span id="LC110" 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;">SeqSlice</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSvPosVector</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC111" 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="n" style="color: #333;">TSvPosVector</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TReadSV</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">TReadSV</span> <span class="n" style="color: #333;">srStore</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;">// Identify SVs</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;">srStore</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="LC116" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Structural Variant Candidates</span></span>
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<pre style="margin: 0;"> <span id="LC118" 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;">StructuralVariantRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TVariants</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">TVariants</span> <span class="n" style="color: #333;">svc</span><span class="p">;</span></span>
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114
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// SR Store</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" 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;">SeqSlice</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSvPosVector</span><span class="p">;</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" 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="n" style="color: #333;">TSvPosVector</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TReadSV</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Temporary split-read store</span></span>
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118
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">TReadSV</span> <span class="n" style="color: #333;">tmpStore</span><span class="p">;</span></span>
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119
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></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;">// SV Discovery</span></span>
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<pre style="margin: 0;"> <span id="LC125" 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>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Assemble</span></span>
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<pre style="margin: 0;"> <span id="LC128" 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>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,54 +141,34 @@ namespace torali {</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">lastSV</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">svIter</span><span class="p">;</span></span>
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138
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">svs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">svIter</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="p">}</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">vcfParse</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="n" style="color: #333;">svs</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Re-genotyping</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" 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="LC142" 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="LC143" 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="LC144" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Re-number SVs</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">sort</span><span class="p">(</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;">svs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">SortSVs</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="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cliqueCount</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="LC148" 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;">TVariants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">svIt</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;">svIt</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;">svIt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cliqueCount</span><span class="p">)</span> <span class="n" style="color: #333;">svIt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cliqueCount</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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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Genotyping</span></span>
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<pre style="margin: 0;">-<span id="LC151" 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;">SeqSlice</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSvPosVector</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC152" 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="n" style="color: #333;">TSvPosVector</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TReadSV</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">TReadSV</span> <span class="n" style="color: #333;">srStore</span><span class="p">;</span></span>
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154
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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;">srStore</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="LC155" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Structural Variant Candidates</span></span>
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<pre style="margin: 0;">-<span id="LC156" 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;">StructuralVariantRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TVariants</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">TVariants</span> <span class="n" style="color: #333;">svc</span><span class="p">;</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Tmp SR Store</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">TReadSV</span> <span class="n" style="color: #333;">tmpStore</span><span class="p">;</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_clusterSRReads(c, validRegions, svc, tmpStore);</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Update srStore</span></span>
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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;">SeqSlice</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSvPosVector</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">-<span id="LC165" 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="n" style="color: #333;">TSvPosVector</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TReadSV</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;">-<span id="LC166" 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;">TReadSV</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">readit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpStore</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">readit</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">tmpStore</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;">readit</span><span class="p">)</span> <span class="p">{</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" 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="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">svIdSet</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;">-<span id="LC168" 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;">readit</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;">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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<td class="diff-line-num old old_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;">-<span id="LC169" 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;">readit</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svid</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TVariants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">itGeno</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;">svs</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</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="n" style="color: #333;">StructuralVariantRecord</span><span class="p">(</span><span class="n" style="color: #333;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">chr</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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</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="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">minRefSep</span><span class="p">),</span> <span class="n" style="color: #333;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">svEnd</span><span class="p">),</span> <span class="n" style="color: #333;">SortSVs</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="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="171" 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">
171
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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="n" style="color: #333;">itGeno</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="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="n" style="color: #333;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">svStart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">itGeno</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">svStart</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;">itGeno</span><span class="p">)</span> <span class="p">{</span></span>
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172
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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;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">itGeno</span><span class="o" style="font-weight: 600;">-></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;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">itGeno</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chr2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</span><span class="p">].</span><span class="n" style="color: #333;">svt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">itGeno</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">svt</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 old old_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">-<span id="LC173" 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;">abs</span><span class="p">(</span><span class="n" style="color: #333;">svc</span><span class="p">[</span><span class="n" style="color: #333;">svid</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;">itGeno</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">minRefSep</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 old old_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">srStore</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">readit</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="n" style="color: #333;">srStore</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="n" style="color: #333;">srStore</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;">readit</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;">TSvPosVector</span><span class="p">()));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Assign read only once to a given SV</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svIdSet</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">itGeno</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">svIdSet</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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<td class="diff-line-num old old_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">-<span id="LC177" 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="LC178" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cerr << readit->first << ':' << svc[svid].chr << ',' << svc[svid].svStart << ',' << svc[svid].chr2 << ',' << svc[svid].svEnd << ',' << svc[svid].svt << ';' << itGeno->chr << ',' << itGeno->svStart << ',' << itGeno->chr2 << ',' << itGeno->svEnd << ',' << itGeno->svt << std::endl;</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">svIdSet</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">itGeno</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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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">readit</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">svid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">itGeno</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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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">srStore</span><span class="p">[</span><span class="n" style="color: #333;">readit</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;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">readit</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;">i</span><span class="p">]);</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"> <span class="p">}</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Sort</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">sort</span><span class="p">(</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;">svs</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">SortSVs</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="p">());</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> </span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Re-number SVs and update SR Store</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" 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;">map</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;">TIdMap</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">TIdMap</span> <span class="n" style="color: #333;">idmap</span><span class="p">;</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cliqueCount</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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152
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<pre style="margin: 0;">+<span id="LC152" 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;">TVariants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">svIt</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;">svIt</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;">svIt</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cliqueCount</span><span class="p">)</span> <span class="p">{</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">idmap</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;">svIt</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;">cliqueCount</span><span class="p">));</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">svIt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cliqueCount</span><span class="p">;</span></span>
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155
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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">
156
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<pre style="margin: 0;">+<span id="LC156" 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;">TReadSV</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpStore</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">tmpStore</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;">ts</span><span class="p">)</span> <span class="p">{</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">keep</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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<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">
158
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<pre style="margin: 0;">+<span id="LC158" 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;">idx</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;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ts</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;">size</span><span class="p">();</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>
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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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idmap</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">ts</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;">idx</span><span class="p">].</span><span class="n" style="color: #333;">svid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">idmap</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="n" style="color: #333;">ts</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;">idx</span><span class="p">].</span><span class="n" style="color: #333;">svid</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>
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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="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="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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">ts</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;">idx</span><span class="p">].</span><span class="n" style="color: #333;">svid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idmap</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">ts</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;">idx</span><span class="p">].</span><span class="n" style="color: #333;">svid</span><span class="p">)</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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<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="n" style="color: #333;">keep</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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184
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="p">}</span></span>
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185
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="p">}</span></span>
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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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keep</span><span class="p">)</span> <span class="n" style="color: #333;">srStore</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ts</span><span class="p">);</span></span>
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186
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="p">}</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//outputStructuralVariants(c, svs);</span></span>
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187
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="p">}</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clean-up</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">
170
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<pre style="margin: 0;">+<span id="LC170" 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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171
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<pre style="margin: 0;">+<span id="LC171" 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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188
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> </span>
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189
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Annotate junction reads</span></span>
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190
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174
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<pre style="margin: 0;"> <span id="LC174" 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;">JunctionCount</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">TSVJunctionMap</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -209,7 +193,8 @@ namespace torali {</td>
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209
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"> <span class="p">}</span></span>
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210
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> </span>
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211
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Reference SV Genotyping</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">trackRef</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">srStore</span><span class="p">,</span> <span class="n" style="color: #333;">jctMap</span><span class="p">,</span> <span class="n" style="color: #333;">rcMap</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//trackRef(c, svs, jctMap, rcMap);</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">genotypeLR</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">srStore</span><span class="p">,</span> <span class="n" style="color: #333;">jctMap</span><span class="p">,</span> <span class="n" style="color: #333;">rcMap</span><span class="p">);</span></span>
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213
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"></span>
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214
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// VCF Output</span></span>
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215
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">vcfOutput</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">svs</span><span class="p">,</span> <span class="n" style="color: #333;">jctMap</span><span class="p">,</span> <span class="n" style="color: #333;">rcMap</span><span class="p">,</span> <span class="n" style="color: #333;">spanMap</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" style="width: 35px; color: rgba(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="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -228,6 +213,7 @@ namespace torali {</td>
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228
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tegua</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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229
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">TeguaConfig</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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230
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215
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<pre style="margin: 0;"> <span id="LC215" 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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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">islr</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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231
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> </span>
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232
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parameter</span></span>
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<pre style="margin: 0;"> <span id="LC219" 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 new_line" data-linenumber="238" style="width: 35px; color: rgba(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">@@ -252,9 +238,15 @@ namespace torali {</td>
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252
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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;">"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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253
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="p">;</span></span>
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>
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241
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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;">options_description</span> <span class="n" style="color: #333;">cons</span><span class="p">(</span><span class="s" style="color: #d14;">"Consensus options"</span><span class="p">);</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">cons</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 new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"max-reads,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;">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;">maxReadPerSV</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;">5</span><span class="p">),</span> <span class="s" style="color: #d14;">"max. reads for consensus computation"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"flank-size,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;">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;">c</span><span class="p">.</span><span class="n" style="color: #333;">minimumFlankSize</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;">400</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. flank size"</span><span class="p">)</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"flank-quality,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;">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;">flankQuality</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;">0.9</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. flank quality"</span><span class="p">)</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="p">;</span> </span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> </span>
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255
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248
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<pre style="margin: 0;"> <span id="LC248" 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;">geno</span><span class="p">(</span><span class="s" style="color: #d14;">"Genotyping options"</span><span class="p">);</span></span>
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256
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">geno</span><span class="p">.</span><span class="n" style="color: #333;">add_options</span><span class="p">()</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"vcffile,v"</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;">vcffile</span><span class="p">),</span> <span class="s" style="color: #d14;">"input VCF/BCF file for genotyping"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
258
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250
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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;">"geno-qual,u"</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;">minGenoQual</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;">5</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. mapping quality for genotyping"</span><span class="p">)</span></span>
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259
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251
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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;">"dump,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="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;">dumpfile</span><span class="p">),</span> <span class="s" style="color: #d14;">"gzipped output file for SV-reads"</span><span class="p">)</span></span>
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260
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252
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<pre style="margin: 0;"> <span id="LC252" 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="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">...</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">@@ -264,8 +256,6 @@ namespace torali {</td>
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256
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<pre style="margin: 0;"> <span id="LC256" 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>
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<td class="diff-line-num old_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">
265
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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
257
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<pre style="margin: 0;"> <span id="LC257" 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;">"graph pruning cutoff"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
266
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<td class="diff-line-num new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"extension,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;">indelExtension</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;">0.5</span><span class="p">),</span> <span class="s" style="color: #d14;">"enforce indel extension"</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="267" 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">
267
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<td class="diff-line-num new_line old" data-linenumber="259" 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="LC267" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"flank-size,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;">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;">c</span><span class="p">.</span><span class="n" style="color: #333;">minimumFlankSize</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;">400</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. flank size"</span><span class="p">)</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"flank-quality,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;">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;">flankQuality</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;">0.9</span><span class="p">),</span> <span class="s" style="color: #d14;">"min. flank quality"</span><span class="p">)</span></span>
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269
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="p">(</span><span class="s" style="color: #d14;">"scoring,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;">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="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">scoring</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;">"3,-2,-3,-1"</span><span class="p">),</span> <span class="s" style="color: #d14;">"alignment scoring"</span><span class="p">)</span></span>
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270
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="p">;</span></span>
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271
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -273,9 +263,9 @@ namespace torali {</td>
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273
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263
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<pre style="margin: 0;"> <span id="LC263" 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>
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274
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> </span>
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275
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265
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<pre style="margin: 0;"> <span id="LC265" 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>
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276
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<pre style="margin: 0;">-<span id="LC276" 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;">disc</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">geno</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>
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266
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<pre style="margin: 0;">+<span id="LC266" 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;">disc</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">cons</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">geno</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>
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277
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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="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>
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<td class="diff-line-num old old_line" data-linenumber="278" 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">
278
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<td class="diff-line-num new_line old" data-linenumber="268" 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="LC278" 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;">disc</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">geno</span><span class="p">);</span></span>
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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 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;">disc</span><span class="p">).</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">cons</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">geno</span><span class="p">);</span></span>
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279
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269
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<pre style="margin: 0;"> <span id="LC269" 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>
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280
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270
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<pre style="margin: 0;"> <span id="LC270" 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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281
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="372" style="width: 35px; color: rgba(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="362" style="width: 35px; color: rgba(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">@@ -372,28 +362,6 @@ namespace torali {</td>
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372
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasExcludeFile</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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373
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"> <span class="p">}</span> <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;">hasExcludeFile</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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374
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> </span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check input VCF file</span></span>
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376
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<pre style="margin: 0;">-<span id="LC376" 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;">"vcffile"</span><span class="p">))</span> <span class="p">{</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" 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;">vcffile</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;">vcffile</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;">vcffile</span><span class="p">)))</span> <span class="p">{</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" 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;">"Input VCF/BCF 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;">vcffile</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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379
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<pre style="margin: 0;">-<span id="LC379" 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>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp"> <span class="p">}</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">htsFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ifile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_open</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">vcffile</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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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ifile</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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383
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<pre style="margin: 0;">-<span id="LC383" 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;">vcffile</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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384
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<pre style="margin: 0;">-<span id="LC384" 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>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"> <span class="p">}</span></span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_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;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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387
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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;">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>
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388
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<pre style="margin: 0;">-<span id="LC388" 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 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;">vcffile</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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389
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<pre style="margin: 0;">-<span id="LC389" 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>
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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">
390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp"> <span class="p">}</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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<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">bcf_close</span><span class="p">(</span><span class="n" style="color: #333;">ifile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">hasVcfFile</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="LC394" class="line" lang="cpp"> <span class="p">}</span> <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;">hasVcfFile</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="LC395" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Check output directory</span></span>
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<pre style="margin: 0;"> <span id="LC366" 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;">_outfileValid</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="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC367" 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">@@ -405,13 +373,8 @@ namespace torali {</td>
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<pre style="margin: 0;"> <span id="LC373" 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="LC374" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Run Tegua</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"pb"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">indelExtension</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.7</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="cpp"> <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="mf" style="color: #099;">0.85</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC411" 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;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ont"</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;">c</span><span class="p">.</span><span class="n" style="color: #333;">indelExtension</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="cpp"> <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="mf" style="color: #099;">0.9</span><span class="p">;</span></span>
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414
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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="LC376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"pb"</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">indelExtension</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.7</span><span class="p">;</span></span>
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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">
377
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<pre style="margin: 0;">+<span id="LC377" 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;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ont"</span><span class="p">)</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">indelExtension</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">runTegua</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#5f65ec0c183df81ed169516d4ec6c5508122dccd"><strong>src/util.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +19,10 @@ namespace torali</td>
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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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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifndef MAX_CN</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define MAX_CN 10</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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="LC26" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC27" 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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<pre style="margin: 0;"> <span id="LC28" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,6 +37,34 @@ namespace torali</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">LibraryInfo</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rs</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">median</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">mad</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">minNormalISize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">minISizeCutoff</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">maxNormalISize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">maxISizeCutoff</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">abnormal_pairs</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="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>
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<pre style="margin: 0;">+<span id="LC40" 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>
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<pre style="margin: 0;">+<span id="LC41" 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>
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<pre style="margin: 0;">+<span id="LC42" 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="LC43" 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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<pre style="margin: 0;">+<span id="LC44" 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>
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<pre style="margin: 0;">+<span id="LC45" 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>
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<pre style="margin: 0;">+<span id="LC46" 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>
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<pre style="margin: 0;">+<span id="LC47" 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>
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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;">qval</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;">double</span> <span class="n" style="color: #333;">cn</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mappable</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sd</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">CNV</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="mi" style="color: #099;">0</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;">ciposlow</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">ciposhigh</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">ciendlow</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">ciendhigh</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">qval</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">mappable</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">sd</span><span class="p">(</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="LC55" 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;">double</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;">double</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;">qval</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;">mappable</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">),</span> <span class="n" style="color: #333;">sd</span><span class="p">(</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="LC56" class="line" lang="cpp"> <span class="p">};</span></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="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="LC59" 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="LC60" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC61" 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="LC62" 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;">cn</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;">cn</span><span class="p">)));</span></span>
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63
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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="p">};</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"></span>
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36
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>
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37
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read count struct</span></span>
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38
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">ReadCount</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,6 +104,8 @@ namespace torali</td>
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72
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<td class="diff-line-num new_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">
104
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<pre style="margin: 0;"> <span id="LC104" 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;">value</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"3to5"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DELLY_SVT_TRANS</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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73
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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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<pre style="margin: 0;"> <span id="LC105" 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;">value</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"5to3"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DELLY_SVT_TRANS</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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74
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</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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107
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<pre style="margin: 0;">+<span id="LC107" 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;">svt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CNV"</span><span class="p">)</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">9</span><span class="p">;</span></span>
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75
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109
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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>
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76
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"3to3"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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77
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111
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<pre style="margin: 0;"> <span id="LC111" 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;">value</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"5to5"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,6 +124,7 @@ namespace torali</td>
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90
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124
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<pre style="margin: 0;"> <span id="LC124" 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="s" style="color: #d14;">"DEL"</span><span class="p">;</span></span>
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91
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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
125
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<pre style="margin: 0;"> <span id="LC125" 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="s" style="color: #d14;">"DUP"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
92
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC126" 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;">4</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_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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<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">
127
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<pre style="margin: 0;">+<span id="LC127" 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;">9</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"CNV"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
93
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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"BND"</span><span class="p">;</span></span>
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94
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="p">}</span></span>
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95
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,7 +165,7 @@ namespace torali</td>
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130
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"></span>
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131
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output directory/file checks</span></span>
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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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167
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<pre style="margin: 0;"> <span id="LC167" 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 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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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">_outfileValid</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;">path</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span> <span class="p">{</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">_outfileValid</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;">path</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;">outfile</span><span class="p">)</span> <span class="p">{</span></span>
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134
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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135
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170
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<pre style="margin: 0;"> <span id="LC170" 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;">outdir</span><span class="p">;</span></span>
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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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">has_parent_path</span><span class="p">())</span> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">parent_path</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/delly/-/commit/faeb27c17a5e3c2645c14c6778f2897982887c26#f92b0b9f2ecd99eca4c19d9518afaae33bc2d58a"><strong>src/version.h</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">@@ -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>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"></span>
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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>
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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">7</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>
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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>
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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>
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