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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/freebayes">Debian Med / freebayes</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/3b14acd35f5feafcc42097dc92ee130c36e5537c">3b14acd3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T13:47:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/0911372c79abfe62553daa3104245984474f733d">0911372c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T13:47:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.1'
Update to upstream version '1.3.1'
with Debian dir e45f2a9bfcd1ed4ceedca3ea11949dd6afc5f8ce</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/178dab77cd15088d6d5e02784ea20b12f97522b5">178dab77</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T13:47:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/9630372f7f3dffcba336aaa26fb332f9dc2d5d3f">9630372f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T13:47:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/4d033e4265c3d51e4165da2e4ae3b97e43338940">4d033e42</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T13:47:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/b76c86e9de8b326ba1f9793e46b701641586875e">b76c86e9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T13:55:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patches, replace use_cpp11.patch by DEB_CFLAGS_MAINT_APPEND=-std=gnu++11 in d/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/47af668f20901b1bb3b43a40707df3d1796fd997">47af668f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T14:18:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: libvcflib-dev (>= 1.0.0~rc2+dfsg-3~) to make sure all binaries needed for testing are available in PATH
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/3e70c88072a9b980e72179a4e48c536d27c3d28e">3e70c880</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T15:18:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip failing test
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/7dcb2b38a2878deadf144ddd994774a11ff2b342">7dcb2b38</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-31T15:21:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>19 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#e7a7b9bd0410f62f4abf4834469772e5b259b4f1">
debian/patches/fix_all_target.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#7900bbc7deb8691929abfe4314ae83c60f651c15">
<span class="new-file">
+
debian/patches/skip_failing_test.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#5bc9cbbed590dad79daca99453ee55850a94307b">
<span class="deleted-file">
−
debian/patches/use_cpp11.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#e27a600b059fb5ae2fdea2749758a974686fd4a1">
debian/patches/use_debian_libs.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#d28d0b42a3d6377c030b233b5666786610f0c31a">
src/AlleleParser.cpp
</a>
</li>
<li class="file-stats">
<a href="#6532bd14206a0c12fa9892041c59ad31412e6d93">
src/AlleleParser.h
</a>
</li>
<li class="file-stats">
<a href="#09a8e11089bd7b184c2ba7778565c1350e1c7e3a">
src/Makefile
</a>
</li>
<li class="file-stats">
<a href="#993e5f267bb8dba90c10539f7d5e8ba6f5876409">
src/Parameters.cpp
</a>
</li>
<li class="file-stats">
<a href="#59d68511ee53779f7d3986f01f6c076fc94153fa">
src/Parameters.h
</a>
</li>
<li class="file-stats">
<a href="#96880c749ae3f3b78a514158e074cbee415d97f4">
src/ResultData.cpp
</a>
</li>
<li class="file-stats">
<a href="#0a8324dd44ff9732a3b3dab3603558762809dc6c">
src/freebayes.cpp
</a>
</li>
<li class="file-stats">
<a href="#b512495eaf318bcd937a386870aed8d1e50a1b0d">
test/t/01_call_variants.t
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#CXXFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1
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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="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">vcflib/Makefile log</span></span>
</pre>
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<td class="diff-line-num old_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">
2
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>src <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span></span>
</pre>
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<td class="diff-line-num old_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">
3
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
</pre>
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<br>
</li>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,6 @@</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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## user manual and guide</span></span>
</pre>
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<td class="diff-line-num old_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="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="markdown"></span>
</pre>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/ekg/freebayes.svg</span><span class="p">)</span>](https://travis-ci.org/ekg/freebayes)</span>
</pre>
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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="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Gitter</span><span class="p">](</span><span class="sx" style="color: #d14;">https://badges.gitter.im/Join</span> Chat.svg)](https://gitter.im/ekg/freebayes?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)</span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">--------</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,8 +23,7 @@ alignments. This method avoids one of the core problems with alignment-based</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown">variant detection--- that identical sequences may have multiple possible </span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown">alignments:</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><img src="http://hypervolu.me/freebayes/figures/haplotype_calling.png" </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown">width=500/></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="nt" style="color: #000080;"><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://github.com/ekg/freebayes/raw/v1.3.0/paper/haplotype_calling.png"</span> <span class="na" style="color: #008080;">width=</span><span class="s" style="color: #d14;">500/</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*FreeBayes*</span> uses short-read alignments </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown">(<span class="p">[</span><span class="nv" style="color: #008080;">BAM</span><span class="p">](</span><span class="sx" style="color: #d14;">http://samtools.sourceforge.net/SAMv1.pdf</span><span class="p">)</span> files with </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">@@ -134,6 +132,26 @@ For a description of available command-line options and their defaults, run:</td>
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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"><span class="sb" style="color: #d14;"> freebayes --help</span></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="gu" style="color: #800080; font-weight: 600;">## Getting the best results</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">freebayes provides many options to configure its operation.</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown">These may be important in certain use cases, but they are not meant for standard use.</span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown">It is strongly recommended that you run freebayes with parameters that are as close to default as possible unless you can validate that the chosen parameters improve performance.</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown">To achieve the desired tradeoff between sensitivity and specificity, the best approach is to filter the output using the <span class="sb" style="color: #d14;">`QUAL`</span> field, which encodes the posterior estimate of the probability of variation.</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown">Filtering the input with the provided options demonstrably hurts performance where truth sets can be used to evaluate results.</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown">By removing information from the input, you can confuse the Bayesian model by making it appear that certain alleles frequently indicative of context specific error (such as indels in homopolymers) don't exist.</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">Many users apply these filters to force freebayes to not make haplotype calls.</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown">This is almost always a mistake, as the haplotype calling process greatly improves the method's signal to noise ratio and normalizes differential alignment in complex regions.</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">If you wish to obtain a VCF that does not contain haplotype calls or complex alleles, first call with default parameters and then decompose the output with tools in vcflib, vt, vcf-tools, bcftools, GATK, and Picard.</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown">Here we use a tool in vcflib that normalizes the haplotype calls into pointwise SNPs and indels:</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"><span class="sb" style="color: #d14;"> freebayes ... | vcfallelicprimitives -kg >calls.vcf</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown">Note that this is not done by default as it makes it difficult to determine which variant calls freebayes completed.</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown">The raw output faithfully describes exactly the calls that were made.</span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Examples</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -145,6 +163,10 @@ Require at least 5 supporting observations to consider a variant:</td>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="markdown"><span class="sb" style="color: #d14;"> freebayes -f ref.fa -C 5 aln.bam >var.vcf</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown">Skip over regions of high depth by discarding alignments overlapping positions where total read depth is greater than 200:</span>
</pre>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="sb" style="color: #d14;"> freebayes -f ref.fa -g 200 aln.bam >var.vcf</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"></span>
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148
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown">Use a different ploidy:</span>
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149
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"><span class="sb" style="color: #d14;"> freebayes -f ref.fa -p 4 aln.bam >var.vcf</span></span>
</pre>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">freebayes (1.3.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Build-Depends: libvcflib-dev (>= 1.0.0~rc2+dfsg-3~) to make sure all</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> binaries needed for testing are available in PATH</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Skip failing test (see</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> https://github.com/ekg/freebayes/issues/329 )</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 31 Jul 2019 17:05:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">freebayes (1.2.0-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,20 +4,20 @@ Uploaders: Brad Chapman <chapmanb@50mail.com>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> zlib1g-dev,</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libbamtools-dev,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> libvcflib-dev (>= 1.0.0~rc2+dfsg-<span class="idiff left right">2</span>~),</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libvcflib-dev (>= 1.0.0~rc2+dfsg-<span class="idiff left right">3</span>~),</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libtabixpp-dev,</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libseqlib-dev,</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> bc,</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="plaintext"> samtools,</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> parallel,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libvcflib-tools (>= 1.0.0~rc1+dfsg1-6)</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.0</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/freebayes</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/freebayes.git</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Homepage: https://github.com/ekg/freebayes</span>
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<li id="e7a7b9bd0410f62f4abf4834469772e5b259b4f1">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#e7a7b9bd0410f62f4abf4834469772e5b259b4f1"><strong>debian/patches/fix_all_target.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,9 +4,12 @@ Description: vcflib needs to be packaged separately</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #CXXFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all: vcflib/Makefile log</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all:<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all:</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> cd src && $(MAKE)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> wbamtools: vcflib/Makefile log</span></pre>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,4 +2,4 @@ use_debian_libs.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_all_target.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_test.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">vcffirstheader.patch</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">use_cpp11</span>.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"><span class="idiff left right">skip_failing_test</span>.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#7900bbc7deb8691929abfe4314ae83c60f651c15"><strong>debian/patches/skip_failing_test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Skip failing test</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> see https://github.com/ekg/freebayes/issues/329</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Wed, 31 Jul 2019 15:47:24 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/test/t/01_call_variants.t</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/t/01_call_variants.t</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span> PATH=../bin:$PATH # for freebayes</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> PATH=../scripts:$PATH # for freebayes-parallel</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> PATH=../vcflib/bin:$PATH # for vcf binaries used by freebayes-parallel</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-plan tests 24</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+plan tests 23</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> is $(echo "$(comm -12 <(cat tiny/NA12878.chr22.tiny.giab.vcf | grep -v "^#" | cut -f 2 | sort) <(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f 2 | sort) | wc -l) >= 13" | bc) 1 "variant calling recovers most of the GiAB variants in a test region"</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -120,4 +120,3 @@</span> is $(freebayes -f tiny/q.fa -F 0.2 tiny/</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> rm -f x.sam</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> is $(freebayes -f tiny/q.fa --skip-coverage 30 tiny/NA12878.chr22.tiny.bam | grep -v '^#' | wc -l) 22 "freebayes makes the expected number of calls when capping coverage"</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-is $(freebayes -f tiny/q.fa -g 30 tiny/NA12878.chr22.tiny.bam | vcfkeepinfo - DP | vcf2tsv | cut -f 8 | tail -n+2 | awk '$1 <= 30 { print }' | wc -l) 22 "all coverage capped calls are below the coverage threshold"</span></span></pre>
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<li id="5bc9cbbed590dad79daca99453ee55850a94307b">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#5bc9cbbed590dad79daca99453ee55850a94307b"><strong>debian/patches/use_cpp11.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Fabian Klötzl <fabian@kloetzl.info></span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Date: Mon, 4 Sep 2017 12:05:00 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Compile as C++11</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> src/Makefile | 2 +-</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff">--- a/src/Makefile</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span> export LIBFLAGS</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> # Compiler flags</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g -std=gnu++11</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`</span></pre>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#e27a600b059fb5ae2fdea2749758a974686fd4a1"><strong>debian/patches/use_debian_libs.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,8 +4,8 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/src/Makefile</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left right">0,14 +20</span>,8 @@</span> export LIBFLAGS</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> <span class="idiff left right">CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left right">1,14 +21</span>,8 @@</span> export LIBFLAGS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-SEQLIB_ROOT=../SeqLib</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">@@ -14,14 +14,14 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LIBS = -lz -llzma -lbz2 -lm -lpthread</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT)<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LIBS = -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp`</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+INCLUDE = -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp`</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> all: autoversion ../bin/freebayes ../bin/bamleftalign</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left right">5,12 +39</span>,6 @@</span> gprof:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left right">6,12 +40</span>,6 @@</span> gprof:</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> .PHONY: all static debug profiling gprof</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </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">@@ -34,7 +34,7 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> OBJECTS=BedReader.o \</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> CNV.o \</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> fastlz.o \</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left right">4,18 +62</span>,7 @@</span> OBJECTS=BedReader.o \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left right">5,18 +63</span>,7 @@</span> OBJECTS=BedReader.o \</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> Bias.o \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> Contamination.o \</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> NonCall.o \</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 +54,7 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> HEADERS=multichoose.h version_git.h</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left right">0,10 +77</span>,10 @@</span> alleles ../bin/alleles: alleles.o $(OBJE</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left right">1,10 +78</span>,10 @@</span> alleles ../bin/alleles: alleles.o $(OBJE</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib)</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> </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">@@ -67,7 +67,7 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left right">8,7 +95</span>,7 @@</span> alleles.o: alleles.cpp AlleleParser.o Al</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left right">9,7 +96</span>,7 @@</span> alleles.o: alleles.cpp AlleleParser.o Al</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> dummy.o: dummy.cpp AlleleParser.o Allele.o</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c dummy.cpp</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> </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 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> fastlz.o: fastlz.c fastlz.h</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">39,7 +116</span>,7 @@</span> Genotype.o: Genotype.cpp Genotype.h Alle</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">40,7 +117</span>,7 @@</span> Genotype.o: Genotype.cpp Genotype.h Alle</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> Ewens.o: Ewens.cpp Ewens.h</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c Ewens.cpp</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> </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">@@ -85,7 +85,7 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c AlleleParser.cpp</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> Utility.o: Utility.cpp Utility.h Sum.h Product.h</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="p">@@ -18<span class="idiff left right">7,22 +164</span>,12 @@</span> bamleftalign.o: bamleftalign.cpp LeftAli</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -18<span class="idiff left right">8,22 +165</span>,12 @@</span> bamleftalign.o: bamleftalign.cpp LeftAli</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"> bamfiltertech.o: bamfiltertech.cpp</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c bamfiltertech.cpp</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> </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">@@ -109,7 +109,7 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"> VERSION_FILE=./version_git.h</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"> RELEASED_VERSION_FILE=./version_release.txt</span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="p">@@ -27<span class="idiff left right">7,5 +244</span>,3 @@</span> autoversion:</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -27<span class="idiff left right">8,5 +245</span>,3 @@</span> autoversion:</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="diff"> </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="diff"> clean:</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="diff"> rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp</span>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND=-std=gnu++11</span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></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="plaintext">%:</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="plaintext"> dh $@ --no-parallel</span>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#d28d0b42a3d6377c030b233b5666786610f0c31a"><strong>src/AlleleParser.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">@@ -1266,19 +1266,16 @@ Allele AlleleParser::makeAllele(RegisteredAlignment& ra,</td>
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1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// a dangerous game</span></span>
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1267
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">currentSequenceStart</span><span class="p">;</span></span>
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1268
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1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minEntropy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">minRepeatEntropy</span><span class="p">;</span></span>
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1269
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<pre style="margin: 0;">-<span id="LC1269" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check first that' wer'e actually ina repeat... TODO</span></span>
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1270
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<pre style="margin: 0;">-<span id="LC1270" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cerr << "entropy of " << entropy(currentSequence.substr(start, repeatRightBoundary - pos)) << " is too low, " << endl;</span></span>
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1271
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1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">minEntropy</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="c1" style="color: #998; font-style: italic;">// ignore if turned off</span></span>
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1272
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<pre style="margin: 0;">-<span id="LC1272" class="line" lang="cpp"> <span class="n" style="color: #333;">repeatRightBoundary</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">currentSequenceStart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">currentSequence</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="c1" style="color: #998; font-style: italic;">//guard</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// don't run off the end of the current sequence</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"> <span class="n" style="color: #333;">repeatRightBoundary</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">currentSequenceStart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">currentSequence</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>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// there is no point in going past the alignment end</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// because we won't make a haplotype call unless we have a covering observation from a read</span></span>
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1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"> <span class="n" style="color: #333;">repeatRightBoundary</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">ENDPOSITION</span> <span class="o" style="font-weight: 600;">&&</span></span>
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1273
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1275
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="cpp"> <span class="n" style="color: #333;">entropy</span><span class="p">(</span><span class="n" style="color: #333;">currentSequence</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">repeatRightBoundary</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="n" style="color: #333;">minEntropy</span><span class="p">)</span> <span class="p">{</span></span>
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1274
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<pre style="margin: 0;">-<span id="LC1274" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cerr << "entropy of " << entropy(currentSequence.substr(start, repeatRightBoundary - pos)) << " is too low, ";</span></span>
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1275
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<pre style="margin: 0;">-<span id="LC1275" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cerr << "increasing rought boundary to ";</span></span>
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1276
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1276
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">repeatRightBoundary</span><span class="p">;</span></span>
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1277
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<pre style="margin: 0;">-<span id="LC1277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cerr << repeatRightBoundary << endl;</span></span>
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1278
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"> <span class="p">}</span></span>
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1279
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"></span>
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1280
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<pre style="margin: 0;">-<span id="LC1280" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// now we</span></span>
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1281
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<pre style="margin: 0;">-<span id="LC1281" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cachedRepeatCounts[pos] = repeatCounts(pos - currentSequenceStart, currentSequence, 12);</span></span>
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1282
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// edge case, the indel is an insertion and matches the reference to the right</span></span>
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1283
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this means there is a repeat structure in the read, but not the ref</span></span>
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1284
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">currentSequence</span><span class="p">.</span><span class="n" style="color: #333;">substr</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;">currentSequenceStart</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">readSequence</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="1992" style="width: 35px; color: rgba(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">@@ -1992,9 +1989,9 @@ void AlleleParser::updateAlignmentQueue(long int position,</td>
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1992
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1989
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<pre style="margin: 0;"> <span id="LC1989" class="line" lang="cpp"> <span class="p">}</span></span>
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1993
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1990
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<pre style="margin: 0;"> <span id="LC1990" class="line" lang="cpp"></span>
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1994
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<td class="diff-line-num new_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1991
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<pre style="margin: 0;"> <span id="LC1991" 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;">gettingPartials</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">ENDPOSITION</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="p">{</span></span>
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1995
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<td class="diff-line-num new_line old" data-linenumber="1992" 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="LC1995" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">QNAME</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" at "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">currentSequenceName</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;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">POSITION</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" is out of order!"</span></span>
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1996
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<pre style="margin: 0;">-<span id="LC1996" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" expected after "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">position</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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1997
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<pre style="margin: 0;">-<span id="LC1997" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); 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="1992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1992
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<pre style="margin: 0;">+<span id="LC1992" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">QNAME</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" at "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">currentSequenceName</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;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">POSITION</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" is out of order!"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1998" style="width: 35px; color: rgba(0,0,0,0.3); 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="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1993
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<pre style="margin: 0;">+<span id="LC1993" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" expected after "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">position</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="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1994
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<pre style="margin: 0;">+<span id="LC1994" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1998
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1995
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<pre style="margin: 0;"> <span id="LC1995" class="line" lang="cpp"> <span class="p">}</span></span>
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1999
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1996
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<pre style="margin: 0;"> <span id="LC1996" class="line" lang="cpp"></span>
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2000
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1997
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<pre style="margin: 0;"> <span id="LC1997" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// otherwise, get the sample name and register the alignment to generate a sequence of alleles</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2022" style="width: 35px; color: rgba(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="2019" style="width: 35px; color: rgba(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">@@ -2022,29 +2019,53 @@ void AlleleParser::updateAlignmentQueue(long int position,</td>
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2022
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2019
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<pre style="margin: 0;"> <span id="LC2019" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">baseQualityCap</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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2023
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2020
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<pre style="margin: 0;"> <span id="LC2020" class="line" lang="cpp"> <span class="n" style="color: #333;">capBaseQuality</span><span class="p">(</span><span class="n" style="color: #333;">currentAlignment</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">baseQualityCap</span><span class="p">);</span></span>
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2024
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2021
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<pre style="margin: 0;"> <span id="LC2021" class="line" lang="cpp"> <span class="p">}</span></span>
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2022
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<pre style="margin: 0;">+<span id="LC2022" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do we exceed coverage anywhere?</span></span>
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2023
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<pre style="margin: 0;">+<span id="LC2023" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do we touch anything where we had exceeded coverage?</span></span>
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2024
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<pre style="margin: 0;">+<span id="LC2024" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if so skip this read, and mark and remove processed alignments and registered alleles overlapping the coverage capped position</span></span>
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2025
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<pre style="margin: 0;">+<span id="LC2025" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">considerAlignment</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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2026
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<pre style="margin: 0;">+<span id="LC2026" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">skipCoverage</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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2027
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<pre style="margin: 0;">+<span id="LC2027" 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;">long</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="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">POSITION</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;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">ENDPOSITION</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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2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">coverage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">skipCoverage</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">gettingPartials</span><span class="p">)</span> <span class="p">{</span></span>
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2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="cpp"> <span class="n" style="color: #333;">considerAlignment</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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2031
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<pre style="margin: 0;">+<span id="LC2031" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// we're exceeding coverage at this position for the first time, so clean up</span></span>
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2032
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<pre style="margin: 0;">+<span id="LC2032" 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;">coverageSkippedPositions</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span> <span class="p">{</span></span>
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2033
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<pre style="margin: 0;">+<span id="LC2033" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// clean up reads overlapping this position</span></span>
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2034
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<pre style="margin: 0;">+<span id="LC2034" class="line" lang="cpp"> <span class="n" style="color: #333;">removeCoverageSkippedAlleles</span><span class="p">(</span><span class="n" style="color: #333;">registeredAlleles</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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2035
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<pre style="margin: 0;">+<span id="LC2035" class="line" lang="cpp"> <span class="n" style="color: #333;">removeCoverageSkippedAlleles</span><span class="p">(</span><span class="n" style="color: #333;">newAlleles</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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2036
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<pre style="margin: 0;">+<span id="LC2036" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// remove the alignments overlapping this position</span></span>
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2037
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<pre style="margin: 0;">+<span id="LC2037" class="line" lang="cpp"> <span class="n" style="color: #333;">removeRegisteredAlignmentsOverlappingPosition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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2038
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<pre style="margin: 0;">+<span id="LC2038" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// record that the position is capped</span></span>
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2039
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<pre style="margin: 0;">+<span id="LC2039" class="line" lang="cpp"> <span class="n" style="color: #333;">coverageSkippedPositions</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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2040
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<pre style="margin: 0;">+<span id="LC2040" class="line" lang="cpp"> <span class="p">}</span></span>
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2041
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<pre style="margin: 0;">+<span id="LC2041" class="line" lang="cpp"> <span class="p">}</span></span>
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2042
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<pre style="margin: 0;">+<span id="LC2042" class="line" lang="cpp"> <span class="p">}</span></span>
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2043
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<pre style="margin: 0;">+<span id="LC2043" class="line" lang="cpp"> <span class="p">}</span></span>
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2025
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2044
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<pre style="margin: 0;"> <span id="LC2044" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// decomposes alignment into a set of alleles</span></span>
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2026
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2045
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<pre style="margin: 0;"> <span id="LC2045" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// here we get the deque of alignments ending at this alignment's end position</span></span>
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2027
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2046
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<pre style="margin: 0;"> <span id="LC2046" class="line" lang="cpp"> <span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">registeredAlignments</span><span class="p">[</span><span class="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">ENDPOSITION</span><span class="p">];</span></span>
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2028
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<pre style="margin: 0;">-<span id="LC2028" class="line" lang="cpp"></span>
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2029
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<pre style="margin: 0;">-<span id="LC2029" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and insert the registered alignment into that deque</span></span>
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2030
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<pre style="margin: 0;">-<span id="LC2030" class="line" lang="cpp"> <span class="n" style="color: #333;">rq</span><span class="p">.</span><span class="n" style="color: #333;">push_front</span><span class="p">(</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="p">(</span><span class="n" style="color: #333;">currentAlignment</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">));</span></span>
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2031
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<pre style="margin: 0;">-<span id="LC2031" class="line" lang="cpp"> <span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rq</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">();</span></span>
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2032
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<pre style="margin: 0;">-<span id="LC2032" class="line" lang="cpp"> <span class="n" style="color: #333;">registerAlignment</span><span class="p">(</span><span class="n" style="color: #333;">currentAlignment</span><span class="p">,</span> <span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">sampleName</span><span class="p">,</span> <span class="n" style="color: #333;">sequencingTech</span><span class="p">);</span></span>
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2033
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<pre style="margin: 0;">-<span id="LC2033" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// backtracking if we have too many mismatches</span></span>
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2034
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<pre style="margin: 0;">-<span id="LC2034" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// or if there are no recorded alleles</span></span>
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2035
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<pre style="margin: 0;">-<span id="LC2035" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span></span>
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2036
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<pre style="margin: 0;">-<span id="LC2036" class="line" lang="cpp"> <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;">ra</span><span class="p">.</span><span class="n" style="color: #333;">mismatches</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;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">SEQLEN</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">readMaxMismatchFraction</span></span>
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2037
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<pre style="margin: 0;">-<span id="LC2037" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">mismatches</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">RMU</span></span>
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2038
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<pre style="margin: 0;">-<span id="LC2038" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">snpCount</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">readSnpLimit</span></span>
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2039
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<pre style="margin: 0;">-<span id="LC2039" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">indelCount</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">readIndelLimit</span><span class="p">)</span> <span class="p">{</span></span>
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2040
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<pre style="margin: 0;">-<span id="LC2040" class="line" lang="cpp"> <span class="n" style="color: #333;">rq</span><span class="p">.</span><span class="n" style="color: #333;">pop_front</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// backtrack</span></span>
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2041
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<pre style="margin: 0;">-<span id="LC2041" 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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2042
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<pre style="margin: 0;">-<span id="LC2042" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// push the alleles into our new alleles vector</span></span>
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2043
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<pre style="margin: 0;">-<span id="LC2043" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">alleles</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;">allele</span><span class="p">)</span> <span class="p">{</span></span>
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2044
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<pre style="margin: 0;">-<span id="LC2044" class="line" lang="cpp"> <span class="n" style="color: #333;">newAlleles</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;">allele</span><span class="p">);</span></span>
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2047
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<pre style="margin: 0;">+<span id="LC2047" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cerr << "parameters capcoverage " << parameters.capCoverage << " " << rq.size() << endl;</span></span>
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2048
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<pre style="margin: 0;">+<span id="LC2048" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">considerAlignment</span><span class="p">)</span> <span class="p">{</span></span>
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2049
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<pre style="margin: 0;">+<span id="LC2049" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and insert the registered alignment into that deque</span></span>
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2050
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<pre style="margin: 0;">+<span id="LC2050" class="line" lang="cpp"> <span class="n" style="color: #333;">rq</span><span class="p">.</span><span class="n" style="color: #333;">push_front</span><span class="p">(</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="p">(</span><span class="n" style="color: #333;">currentAlignment</span><span class="p">));</span></span>
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2051
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<pre style="margin: 0;">+<span id="LC2051" class="line" lang="cpp"> <span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rq</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">();</span></span>
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2052
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<pre style="margin: 0;">+<span id="LC2052" class="line" lang="cpp"> <span class="n" style="color: #333;">registerAlignment</span><span class="p">(</span><span class="n" style="color: #333;">currentAlignment</span><span class="p">,</span> <span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">sampleName</span><span class="p">,</span> <span class="n" style="color: #333;">sequencingTech</span><span class="p">);</span></span>
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2053
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<pre style="margin: 0;">+<span id="LC2053" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// backtracking if we have too many mismatches</span></span>
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2054
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<pre style="margin: 0;">+<span id="LC2054" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// or if there are no recorded alleles</span></span>
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2055
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<pre style="margin: 0;">+<span id="LC2055" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span></span>
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2056
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<pre style="margin: 0;">+<span id="LC2056" class="line" lang="cpp"> <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;">ra</span><span class="p">.</span><span class="n" style="color: #333;">mismatches</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;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">SEQLEN</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">readMaxMismatchFraction</span></span>
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2057
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<pre style="margin: 0;">+<span id="LC2057" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">mismatches</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">RMU</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2058
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<pre style="margin: 0;">+<span id="LC2058" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">snpCount</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">readSnpLimit</span></span>
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2059
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<pre style="margin: 0;">+<span id="LC2059" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">indelCount</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">readIndelLimit</span><span class="p">)</span> <span class="p">{</span></span>
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2060
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<pre style="margin: 0;">+<span id="LC2060" class="line" lang="cpp"> <span class="n" style="color: #333;">rq</span><span class="p">.</span><span class="n" style="color: #333;">pop_front</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// backtrack</span></span>
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2061
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<pre style="margin: 0;">+<span id="LC2061" 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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2062
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<pre style="margin: 0;">+<span id="LC2062" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// push the alleles into our new alleles vector</span></span>
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2063
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<pre style="margin: 0;">+<span id="LC2063" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">alleles</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;">allele</span><span class="p">)</span> <span class="p">{</span></span>
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2064
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<pre style="margin: 0;">+<span id="LC2064" class="line" lang="cpp"> <span class="n" style="color: #333;">newAlleles</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;">allele</span><span class="p">);</span></span>
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2065
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<pre style="margin: 0;">+<span id="LC2065" class="line" lang="cpp"> <span class="p">}</span></span>
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2045
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2066
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<pre style="margin: 0;"> <span id="LC2066" class="line" lang="cpp"> <span class="p">}</span></span>
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2046
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2067
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="cpp"> <span class="p">}</span></span>
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2047
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<pre style="margin: 0;">-<span id="LC2047" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="p">}</span></span>
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2068
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<pre style="margin: 0;">+<span id="LC2068" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="p">}</span></span>
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2048
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2069
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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">hasMoreAlignments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GETNEXT</span><span class="p">(</span><span class="n" style="color: #333;">bamMultiReader</span><span class="p">,</span> <span class="n" style="color: #333;">currentAlignment</span><span class="p">))</span></span>
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2049
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2070
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<pre style="margin: 0;"> <span id="LC2070" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">POSITION</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">position</span></span>
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2050
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2071
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<pre style="margin: 0;"> <span id="LC2071" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">REFID</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">currentRefID</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2054" style="width: 35px; color: rgba(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">@@ -2054,6 +2075,44 @@ void AlleleParser::updateAlignmentQueue(long int position,</td>
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2054
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2075
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<pre style="margin: 0;"> <span id="LC2075" class="line" lang="cpp"></span>
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2055
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2076
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<pre style="margin: 0;"> <span id="LC2076" class="line" lang="cpp"><span class="p">}</span></span>
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2056
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2077
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<pre style="margin: 0;"> <span id="LC2077" class="line" lang="cpp"></span>
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2078
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<pre style="margin: 0;">+<span id="LC2078" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AlleleParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">removeRegisteredAlignmentsOverlappingPosition</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</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;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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2079
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<pre style="margin: 0;">+<span id="LC2079" class="line" lang="cpp"> <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;">long</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="p">,</span> <span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">registeredAlignments</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="cpp"> <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;">long</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="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alignmentsToErase</span><span class="p">;</span></span>
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2081
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<pre style="margin: 0;">+<span id="LC2081" class="line" lang="cpp"> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">allelesToErase</span><span class="p">;</span></span>
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2082
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<pre style="margin: 0;">+<span id="LC2082" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">registeredAlignments</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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2083
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<pre style="margin: 0;">+<span id="LC2083" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</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;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">f</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;">end</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="p">{</span></span>
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2084
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<pre style="margin: 0;">+<span id="LC2084" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">d</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;">pos</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">d</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;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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2085
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<pre style="margin: 0;">+<span id="LC2085" class="line" lang="cpp"> <span class="n" style="color: #333;">alignmentsToErase</span><span class="p">[</span><span class="n" style="color: #333;">f</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;">insert</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">);</span></span>
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2086
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<pre style="margin: 0;">+<span id="LC2086" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alleles</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;">a</span><span class="p">)</span> <span class="p">{</span></span>
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2087
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<pre style="margin: 0;">+<span id="LC2087" class="line" lang="cpp"> <span class="n" style="color: #333;">allelesToErase</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;">a</span><span class="p">);</span></span>
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2088
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<pre style="margin: 0;">+<span id="LC2088" class="line" lang="cpp"> <span class="p">}</span></span>
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2089
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="cpp"> <span class="p">}</span></span>
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2090
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="cpp"> <span class="p">}</span></span>
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2091
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<pre style="margin: 0;">+<span id="LC2091" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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2092
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<pre style="margin: 0;">+<span id="LC2092" class="line" lang="cpp"> <span class="p">}</span></span>
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2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// clean up registered alleles--- maybe this should be done externally?</span></span>
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2094
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">registeredAlleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">registeredAlleles</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;">a</span><span class="p">)</span> <span class="p">{</span></span>
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2095
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<pre style="margin: 0;">+<span id="LC2095" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allelesToErase</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2096
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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</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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2097
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="cpp"> <span class="p">}</span></span>
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2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="cpp"> <span class="p">}</span></span>
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2099
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="cpp"> <span class="n" style="color: #333;">registeredAlleles</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">registeredAlleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">registeredAlleles</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="p">(</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span> <span class="n" style="color: #333;">registeredAlleles</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="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2100
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<pre style="margin: 0;">+<span id="LC2100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alignmentsToErase</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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<td class="diff-line-num new new_line" data-linenumber="2101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2101
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<pre style="margin: 0;">+<span id="LC2101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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;">long</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="p">,</span> <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignmentsToErase</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2102
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<pre style="margin: 0;">+<span id="LC2102" class="line" lang="cpp"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">alignmentsToErase</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;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2103
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<pre style="margin: 0;">+<span id="LC2103" class="line" lang="cpp"> <span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">updated</span><span class="p">;</span></span>
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2104
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<pre style="margin: 0;">+<span id="LC2104" class="line" lang="cpp"> <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;">long</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="p">,</span> <span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">registeredAlignments</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2105
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<pre style="margin: 0;">+<span id="LC2105" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">registeredAlignments</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="2106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2106
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<pre style="margin: 0;">+<span id="LC2106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</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;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">f</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;">end</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2107
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<pre style="margin: 0;">+<span id="LC2107" 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;">e</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;">count</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2108
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<pre style="margin: 0;">+<span id="LC2108" class="line" lang="cpp"> <span class="n" style="color: #333;">updated</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;">d</span><span class="p">);</span></span>
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2109
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<pre style="margin: 0;">+<span id="LC2109" class="line" lang="cpp"> <span class="p">}</span></span>
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2110
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<pre style="margin: 0;">+<span id="LC2110" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2111
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<pre style="margin: 0;">+<span id="LC2111" class="line" lang="cpp"> <span class="n" style="color: #333;">f</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;">updated</span><span class="p">;</span></span>
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2112
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<pre style="margin: 0;">+<span id="LC2112" class="line" lang="cpp"> <span class="p">}</span></span>
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2113
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<pre style="margin: 0;">+<span id="LC2113" class="line" lang="cpp"> <span class="p">}</span></span>
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2114
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<pre style="margin: 0;">+<span id="LC2114" class="line" lang="cpp"><span class="p">}</span></span>
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2115
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<pre style="margin: 0;">+<span id="LC2115" class="line" lang="cpp"> </span>
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2116
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<pre style="margin: 0;"> <span id="LC2116" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AlleleParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addToRegisteredAlleles</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">alleles</span><span class="p">)</span> <span class="p">{</span></span>
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2058
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2117
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<pre style="margin: 0;"> <span id="LC2117" class="line" lang="cpp"> <span class="n" style="color: #333;">registeredAlleles</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">registeredAlleles</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span></span>
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2118
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<pre style="margin: 0;"> <span id="LC2118" class="line" lang="cpp"> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</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">@@ -2505,6 +2564,17 @@ void AlleleParser::removePreviousAlleles(vector<Allele*>& alleles, long int posi</td>
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2505
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2564
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<pre style="margin: 0;"> <span id="LC2564" class="line" lang="cpp"> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="p">(</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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2506
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2565
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<pre style="margin: 0;"> <span id="LC2565" class="line" lang="cpp"><span class="p">}</span></span>
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2507
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2566
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<pre style="margin: 0;"> <span id="LC2566" class="line" lang="cpp"></span>
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2567
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<pre style="margin: 0;">+<span id="LC2567" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AlleleParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">removeCoverageSkippedAlleles</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">alleles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="p">{</span></span>
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2568
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<pre style="margin: 0;">+<span id="LC2568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">alleles</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;">a</span><span class="p">)</span> <span class="p">{</span></span>
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2569
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<pre style="margin: 0;">+<span id="LC2569" class="line" lang="cpp"> <span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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2570
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<pre style="margin: 0;">+<span id="LC2570" 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;">a</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignmentStart</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alignmentEnd</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="p">{</span></span>
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2571
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<pre style="margin: 0;">+<span id="LC2571" class="line" lang="cpp"> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">processed</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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2572
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<pre style="margin: 0;">+<span id="LC2572" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</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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2573
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<pre style="margin: 0;">+<span id="LC2573" class="line" lang="cpp"> <span class="p">}</span></span>
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2574
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<pre style="margin: 0;">+<span id="LC2574" class="line" lang="cpp"> <span class="p">}</span></span>
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2575
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<pre style="margin: 0;">+<span id="LC2575" class="line" lang="cpp"> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="p">(</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span> <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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2576
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<pre style="margin: 0;">+<span id="LC2576" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2577" class="line" lang="cpp"></span>
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2508
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2578
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<pre style="margin: 0;"> <span id="LC2578" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// steps our position/beddata/reference pointers through all positions in all</span></span>
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2509
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<td class="diff-line-num new_line" data-linenumber="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2579
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<pre style="margin: 0;"> <span id="LC2579" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// targets, returns false when we are finished</span></span>
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2510
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2580
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<pre style="margin: 0;"> <span id="LC2580" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2518" style="width: 35px; color: rgba(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="2588" style="width: 35px; color: rgba(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">@@ -2518,6 +2588,9 @@ bool AlleleParser::toNextTarget(void) {</td>
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2518
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2588
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<pre style="margin: 0;"> <span id="LC2588" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"to next target"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2519
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2589
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<pre style="margin: 0;"> <span id="LC2589" class="line" lang="cpp"></span>
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2520
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<td class="diff-line-num new_line" data-linenumber="2590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2590
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<pre style="margin: 0;"> <span id="LC2590" class="line" lang="cpp"> <span class="n" style="color: #333;">clearRegisteredAlignments</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); 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="2591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2591
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<pre style="margin: 0;">+<span id="LC2591" class="line" lang="cpp"> <span class="n" style="color: #333;">coverageSkippedPositions</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); 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="2592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2592
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<pre style="margin: 0;">+<span id="LC2592" class="line" lang="cpp"> <span class="n" style="color: #333;">cachedRepeatCounts</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2593
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<pre style="margin: 0;">+<span id="LC2593" class="line" lang="cpp"> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2521
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2594
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<pre style="margin: 0;"> <span id="LC2594" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2522
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2595
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<pre style="margin: 0;"> <span id="LC2595" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reset haplotype length; there is no last call in this sequence; it isn't relevant</span></span>
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<td class="diff-line-num old_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2523
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<td class="diff-line-num new_line" data-linenumber="2596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2596
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<pre style="margin: 0;"> <span id="LC2596" class="line" lang="cpp"> <span class="n" style="color: #333;">lastHaplotypeLength</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="2763" style="width: 35px; color: rgba(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="2836" style="width: 35px; color: rgba(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">@@ -2763,6 +2836,9 @@ bool AlleleParser::toNextPosition(void) {</td>
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<td class="diff-line-num old_line" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2763
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<td class="diff-line-num new_line" data-linenumber="2836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2836
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<pre style="margin: 0;"> <span id="LC2836" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">registeredAlignments</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">currentRefID</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">currentAlignment</span><span class="p">.</span><span class="n" style="color: #333;">REFID</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2764
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<td class="diff-line-num new_line" data-linenumber="2837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2837
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<pre style="margin: 0;"> <span id="LC2837" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"at end of sequence"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2765
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<td class="diff-line-num new_line" data-linenumber="2838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2838
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<pre style="margin: 0;"> <span id="LC2838" class="line" lang="cpp"> <span class="n" style="color: #333;">clearRegisteredAlignments</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2839
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<pre style="margin: 0;">+<span id="LC2839" class="line" lang="cpp"> <span class="n" style="color: #333;">coverageSkippedPositions</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2766" style="width: 35px; color: rgba(0,0,0,0.3); 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="2840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2840
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<pre style="margin: 0;">+<span id="LC2840" class="line" lang="cpp"> <span class="n" style="color: #333;">cachedRepeatCounts</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2841
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<pre style="margin: 0;">+<span id="LC2841" class="line" lang="cpp"> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
</pre>
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2766
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<td class="diff-line-num new_line" data-linenumber="2842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2842
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<pre style="margin: 0;"> <span id="LC2842" class="line" lang="cpp"> <span class="n" style="color: #333;">loadNextPositionWithAlignmentOrInputVariant</span><span class="p">(</span><span class="n" style="color: #333;">currentAlignment</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2767
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<td class="diff-line-num new_line" data-linenumber="2843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2843
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<pre style="margin: 0;"> <span id="LC2843" class="line" lang="cpp"> <span class="n" style="color: #333;">justSwitchedTargets</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 old_line" data-linenumber="2768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2768
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<td class="diff-line-num new_line" data-linenumber="2844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2844
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<pre style="margin: 0;"> <span id="LC2844" 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="2799" style="width: 35px; color: rgba(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">@@ -2799,11 +2875,6 @@ bool AlleleParser::toNextPosition(void) {</td>
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2799
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2875
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<pre style="margin: 0;"> <span id="LC2875" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// done typically at each new read, but this handles the case where there is no data for a while</span></span>
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2800
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2876
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<pre style="margin: 0;"> <span id="LC2876" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//updateInputVariants(currentPosition, 1);</span></span>
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2801
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2877
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<pre style="margin: 0;"> <span id="LC2877" class="line" lang="cpp"></span>
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2802
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<pre style="margin: 0;">-<span id="LC2802" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//DEBUG2("updating registered alleles");</span></span>
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2803
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<pre style="margin: 0;">-<span id="LC2803" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//updateRegisteredAlleles(); // this removes unused left-flanking sequence</span></span>
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2804
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<pre style="margin: 0;">-<span id="LC2804" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//DEBUG2("updating prior variant alleles");</span></span>
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2805
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<pre style="margin: 0;">-<span id="LC2805" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//updatePriorAlleles();</span></span>
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2806
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<pre style="margin: 0;">-<span id="LC2806" class="line" lang="cpp"></span>
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2807
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2878
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<pre style="margin: 0;"> <span id="LC2878" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// remove past registered alleles</span></span>
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2808
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2879
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<pre style="margin: 0;"> <span id="LC2879" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG2</span><span class="p">(</span><span class="s" style="color: #d14;">"marking previous alleles as processed and removing from registered alleles"</span><span class="p">);</span></span>
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2809
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2880
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<pre style="margin: 0;"> <span id="LC2880" class="line" lang="cpp"> <span class="n" style="color: #333;">removePreviousAlleles</span><span class="p">(</span><span class="n" style="color: #333;">registeredAlleles</span><span class="p">,</span> <span class="n" style="color: #333;">currentPosition</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">@@ -2861,6 +2932,17 @@ bool AlleleParser::toNextPosition(void) {</td>
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2861
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2932
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<pre style="margin: 0;"> <span id="LC2932" class="line" lang="cpp"> <span class="n" style="color: #333;">cachedRepeatCounts</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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2862
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2933
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<pre style="margin: 0;"> <span id="LC2933" class="line" lang="cpp"> <span class="p">}</span></span>
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2863
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2934
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<pre style="margin: 0;"> <span id="LC2934" class="line" lang="cpp"></span>
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2935
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<pre style="margin: 0;">+<span id="LC2935" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG2</span><span class="p">(</span><span class="s" style="color: #d14;">"erasing old coverage cap"</span><span class="p">);</span></span>
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2936
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<pre style="margin: 0;">+<span id="LC2936" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">coverageSkippedPositions</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">coverageSkippedPositions</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">currentPosition</span><span class="p">)</span> <span class="p">{</span></span>
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2937
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<pre style="margin: 0;">+<span id="LC2937" class="line" lang="cpp"> <span class="n" style="color: #333;">coverageSkippedPositions</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">coverageSkippedPositions</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">());</span></span>
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2938
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<pre style="margin: 0;">+<span id="LC2938" class="line" lang="cpp"> <span class="p">}</span></span>
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2939
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<pre style="margin: 0;">+<span id="LC2939" class="line" lang="cpp"></span>
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2940
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<pre style="margin: 0;">+<span id="LC2940" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG2</span><span class="p">(</span><span class="s" style="color: #d14;">"erasing old coverage counts"</span><span class="p">);</span></span>
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2941
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<pre style="margin: 0;">+<span id="LC2941" class="line" lang="cpp"> <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;">long</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</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="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span></span>
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2942
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<pre style="margin: 0;">+<span id="LC2942" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">cov</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">coverage</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;">cov</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">currentPosition</span><span class="p">)</span> <span class="p">{</span></span>
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2943
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<pre style="margin: 0;">+<span id="LC2943" class="line" lang="cpp"> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">cov</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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2944
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<pre style="margin: 0;">+<span id="LC2944" class="line" lang="cpp"> <span class="p">}</span></span>
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2945
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<pre style="margin: 0;">+<span id="LC2945" class="line" lang="cpp"></span>
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2864
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2946
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<pre style="margin: 0;"> <span id="LC2946" 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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2865
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2947
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<pre style="margin: 0;"> <span id="LC2947" class="line" lang="cpp"></span>
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2866
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2948
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<pre style="margin: 0;"> <span id="LC2948" 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="3139" style="width: 35px; color: rgba(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="3221" style="width: 35px; color: rgba(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">@@ -3139,7 +3221,7 @@ void AlleleParser::buildHaplotypeAlleles(</td>
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3139
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3221
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<pre style="margin: 0;"> <span id="LC3221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ras</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ras</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;">r</span><span class="p">)</span> <span class="p">{</span></span>
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3140
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3222
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<pre style="margin: 0;"> <span id="LC3222" class="line" lang="cpp"> <span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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3141
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3223
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<pre style="margin: 0;"> <span id="LC3223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">ra</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;">currentPosition</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ra</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;">currentPosition</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">haplotypeLength</span><span class="p">)</span></span>
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3142
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<pre style="margin: 0;">-<span id="LC3142" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ra</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;">currentPosition</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ra</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;">currentPosition</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">haplotypeLength</span><span class="p">))</span> <span class="p">{</span></span>
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3224
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<pre style="margin: 0;">+<span id="LC3224" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">ra</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;">currentPosition</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ra</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;">currentPosition</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">haplotypeLength</span><span class="p">))</span> <span class="p">{</span></span>
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3143
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3225
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<pre style="margin: 0;"> <span id="LC3225" class="line" lang="cpp"> <span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">aptr</span><span class="p">;</span></span>
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3144
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3226
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<pre style="margin: 0;"> <span id="LC3226" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">allowPartials</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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3145
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3227
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<pre style="margin: 0;"> <span id="LC3227" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">fitHaplotype</span><span class="p">(</span><span class="n" style="color: #333;">currentPosition</span><span class="p">,</span> <span class="n" style="color: #333;">haplotypeLength</span><span class="p">,</span> <span class="n" style="color: #333;">aptr</span><span class="p">,</span> <span class="n" style="color: #333;">allowPartials</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3553" style="width: 35px; color: rgba(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="3635" style="width: 35px; color: rgba(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">@@ -3553,11 +3635,12 @@ bool AlleleParser::getNextAlleles(Samples& samples, int allowedAlleleTypes) {</td>
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3553
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3635
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<pre style="margin: 0;"> <span id="LC3635" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AlleleParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getAlleles</span><span class="p">(</span><span class="n" style="color: #333;">Samples</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">samples</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allowedAlleleTypes</span><span class="p">,</span></span>
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3554
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3636
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<pre style="margin: 0;"> <span id="LC3636" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">haplotypeLength</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">getAllAllelesInHaplotype</span><span class="p">,</span></span>
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3555
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3637
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<pre style="margin: 0;"> <span id="LC3637" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ignoreProcessedFlag</span><span class="p">)</span> <span class="p">{</span></span>
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3556
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<pre style="margin: 0;">-<span id="LC3556" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC3638" class="line" lang="cpp"> <span class="n" style="color: #333;">Samples</span> <span class="n" style="color: #333;">gvcf_held</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// make some samples that by bass filtering for gvcf lines</span></span>
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3557
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3639
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<pre style="margin: 0;"> <span id="LC3639" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG2</span><span class="p">(</span><span class="s" style="color: #d14;">"getting alleles"</span><span class="p">);</span></span>
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3558
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<pre style="margin: 0;">-<span id="LC3558" class="line" lang="cpp"></span>
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3559
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<pre style="margin: 0;">-<span id="LC3559" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">Samples</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</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;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">s</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;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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3560
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<pre style="margin: 0;">-<span id="LC3560" class="line" lang="cpp"> <span class="n" style="color: #333;">s</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;">clear</span><span class="p">();</span></span>
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3640
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<pre style="margin: 0;">+<span id="LC3640" class="line" lang="cpp"> <span class="n" style="color: #333;">samples</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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3641
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<pre style="margin: 0;">+<span id="LC3641" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Commenting this out and replacinf with .clear() to relly empty it, it is more aloc, but no major change</span></span>
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3642
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<pre style="margin: 0;">+<span id="LC3642" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for (Samples::iterator s = samples.begin(); s != samples.end(); ++s)</span></span>
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3643
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<pre style="margin: 0;">+<span id="LC3643" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// s->second.clear();</span></span>
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3561
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3644
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<pre style="margin: 0;"> <span id="LC3644" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO ^^^ this should be optimized for better scanning performance</span></span>
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3562
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3645
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<pre style="margin: 0;"> <span id="LC3645" class="line" lang="cpp"></span>
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3563
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3646
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<pre style="margin: 0;"> <span id="LC3646" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if we have targets and are outside of the current target, don't return anything</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3600" style="width: 35px; color: rgba(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="3683" style="width: 35px; color: rgba(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">@@ -3600,6 +3683,9 @@ void AlleleParser::getAlleles(Samples& samples, int allowedAlleleTypes,</td>
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3600
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3683
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<pre style="margin: 0;"> <span id="LC3683" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">currentPosition</span><span class="p">)))</span></span>
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3601
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3684
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<pre style="margin: 0;"> <span id="LC3684" class="line" lang="cpp"> <span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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3602
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3685
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<pre style="margin: 0;"> <span id="LC3685" class="line" lang="cpp"> <span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">haplotypeLength</span><span class="p">);</span></span>
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3686
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<pre style="margin: 0;">+<span id="LC3686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFout</span><span class="p">){</span></span>
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3687
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<pre style="margin: 0;">+<span id="LC3687" class="line" lang="cpp"> <span class="n" style="color: #333;">gvcf_held</span><span class="p">[</span><span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">sampleID</span><span class="p">][</span><span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">currentBase</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;">a</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// store things incase</span></span>
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3688
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<pre style="margin: 0;">+<span id="LC3688" class="line" lang="cpp"> <span class="p">}</span></span>
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3603
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3689
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<pre style="margin: 0;"> <span id="LC3689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">quality</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">BQL0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">currentBase</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"N"</span></span>
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3690
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<pre style="margin: 0;"> <span id="LC3690" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">isReference</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">allele</span><span class="p">.</span><span class="n" style="color: #333;">alternateSequence</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// filters haplotype construction chaff</span></span>
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3691
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<pre style="margin: 0;"> <span id="LC3691" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cerr << "keeping allele " << allele << 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">@@ -3619,6 +3705,9 @@ void AlleleParser::getAlleles(Samples& samples, int allowedAlleleTypes,</td>
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3619
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3705
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<pre style="margin: 0;"> <span id="LC3705" class="line" lang="cpp"> <span class="p">}</span></span>
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3620
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3706
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<pre style="margin: 0;"> <span id="LC3706" class="line" lang="cpp"> <span class="p">}</span></span>
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3621
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3707
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<pre style="margin: 0;"> <span id="LC3707" class="line" lang="cpp"> <span class="p">}</span></span>
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3708
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<pre style="margin: 0;">+<span id="LC3708" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">samples</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;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFout</span><span class="p">){</span></span>
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3709
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<pre style="margin: 0;">+<span id="LC3709" class="line" lang="cpp"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gvcf_held</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// if there are no non reference vals try to recover any allined values for gvcf if doing gvcf output!!</span></span>
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3710
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<pre style="margin: 0;">+<span id="LC3710" class="line" lang="cpp"> <span class="p">}</span></span>
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3711
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<pre style="margin: 0;"> <span id="LC3711" class="line" lang="cpp"></span>
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3712
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<pre style="margin: 0;"> <span id="LC3712" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</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;">samplesToErase</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3713" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// now remove empty alleles from our return so as to not confuse processing</span></span>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#6532bd14206a0c12fa9892041c59ad31412e6d93"><strong>src/AlleleParser.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">@@ -57,10 +57,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">snpCount</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">indelCount</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alleleTypes</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">Parameters</span> <span class="n" style="color: #333;">parameters</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">RegisteredAlignment</span><span class="p">(</span><span class="n" style="color: #333;">BAMALIGN</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alignment</span><span class="p">,</span> <span class="n" style="color: #333;">Parameters</span> <span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//: alignment(alignment)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">RegisteredAlignment</span><span class="p">(</span><span class="n" style="color: #333;">BAMALIGN</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <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;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">POSITION</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="c"> <span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">ENDPOSITION</span><span class="p">)</span></span>
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66
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="p">,</span> <span class="n" style="color: #333;">refid</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">.</span><span class="n" style="color: #333;">REFID</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">@@ -69,7 +67,6 @@ public:</td>
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69
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="p">,</span> <span class="n" style="color: #333;">snpCount</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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70
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="p">,</span> <span class="n" style="color: #333;">indelCount</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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71
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="p">,</span> <span class="n" style="color: #333;">alleleTypes</span><span class="p">(</span><span class="mi" style="color: #099;">0</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="c"> <span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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73
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> <span class="p">{</span></span>
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74
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">FILLREADGROUP</span><span class="p">(</span><span class="n" style="color: #333;">readgroup</span><span class="p">,</span> <span class="n" style="color: #333;">alignment</span><span class="p">);</span></span>
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75
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,6 +192,8 @@ public:</td>
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195
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"></span>
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196
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">registeredAlleles</span><span class="p">;</span></span>
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197
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <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;">long</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="p">,</span> <span class="n" style="color: #333;">deque</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RegisteredAlignment</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">registeredAlignments</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="c"> <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;">long</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="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">coverageSkippedPositions</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="c"> <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;">long</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</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="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">coverage</span><span class="p">;</span></span>
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198
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <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;">int</span><span class="p">,</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;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">inputVariantAlleles</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// all variants present in the input VCF, as 'genotype' alleles</span></span>
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199
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <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;">int</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</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;">nextInputVariantPosition</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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200
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">getInputVariantsInRegion</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">end</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="251" style="width: 35px; color: rgba(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="250" style="width: 35px; color: rgba(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">@@ -251,6 +250,8 @@ public:</td>
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251
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">haplotypeLength</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="LC251" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getAllAllelesInHaplotype</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="LC252" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removePreviousAlleles</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">alleles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">position</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeCoverageSkippedAlleles</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">alleles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">position</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeRegisteredAlignmentsOverlappingPosition</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</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;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeFilteredAlleles</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">alleles</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="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeDuplicateAlleles</span><span class="p">(</span><span class="n" style="color: #333;">Samples</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;">map</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">alleleGroups</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allowedAlleleTypes</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">haplotypeLength</span><span class="p">,</span> <span class="n" style="color: #333;">Allele</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">refallele</span><span class="p">);</span></span>
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<li id="09a8e11089bd7b184c2ba7778565c1350e1c7e3a">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#09a8e11089bd7b184c2ba7778565c1350e1c7e3a"><strong>src/Makefile</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">@@ -5,6 +5,8 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Compiler</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-ggdb</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">CXX</span><span class="o" style="font-weight: 600;">=</span>g++ <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CXXFLAGS</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">C</span><span class="o" style="font-weight: 600;">=</span>gcc</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></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">@@ -17,7 +19,6 @@ export LIBFLAGS</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Compiler flags</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="nt" style="color: #000080;">-g</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="nv" style="color: #008080;">SEQLIB_ROOT</span><span class="o" style="font-weight: 600;">=</span>../SeqLib</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">@@ -26,13 +27,13 @@ TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"><span class="nv" style="color: #008080;">HTSLIB_ROOT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(SEQLIB_ROOT)</span>/htslib</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"><span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-lz</span> <span class="nt" style="color: #000080;">-llzma</span> <span class="nt" style="color: #000080;">-lbz2</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lpthread</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="make"><span class="nv" style="color: #008080;">INCLUDE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-I</span>../src <span class="nt" style="color: #000080;">-I</span>../ttmath <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/src/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/smithwaterman/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/multichoose/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/filevercmp/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/fastahack/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(HTSLIB_ROOT)</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(SEQLIB_ROOT)</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"><span class="nv" style="color: #008080;">INCLUDE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-I</span>../src <span class="nt" style="color: #000080;">-I</span>../ttmath <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/src/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/smithwaterman/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/multichoose/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/filevercmp/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCFLIB_ROOT)</span>/fastahack/ <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(HTSLIB_ROOT)</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(SEQLIB_ROOT)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">autoversion ../bin/freebayes ../bin/bamleftalign</span></span>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nl">static</span><span class="o" style="font-weight: 600;">:</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(CXXFLAGS)</span><span class="s2" style="color: #d14;"> -static"</span> all</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(CXXFLAGS)</span><span class="s2" style="color: #d14;"> -static<span class="idiff left right"> -static-libstdc++ -static-libgcc -Wl,--allow-multiple-definition</span>"</span> all</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="nl">debug</span><span class="o" style="font-weight: 600;">:</span></span>
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38
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="nv" style="color: #008080;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(CXXFLAGS)</span><span class="s2" style="color: #d14;"> -D VERBOSE_DEBUG -g -rdynamic"</span> all</span>
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<li id="993e5f267bb8dba90c10539f7d5e8ba6f5876409">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#993e5f267bb8dba90c10539f7d5e8ba6f5876409"><strong>src/Parameters.cpp</strong></a>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,6 +72,9 @@ void Parameters::usage(char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" # require at least 5 supporting observations to consider a variant"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" freebayes -f ref.fa -C 5 aln.bam >var.vcf"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" # discard alignments overlapping positions where total read depth is greater than 200"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" freebayes -f ref.fa -g 200 aln.bam >var.vcf"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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75
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" # use a different ploidy"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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76
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" freebayes -f ref.fa -p 4 aln.bam >var.vcf"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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77
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,11 +129,12 @@ void Parameters::usage(char** argv) {</td>
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126
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -A --cnv-map FILE"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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127
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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="s" style="color: #d14;">" Read a copy number map from the BED file FILE, which has"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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128
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" either a sample-level ploidy:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" sample<span class="idiff left right"> name, copy </span>number"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" sample<span class="idiff left right">_name copy_</span>number"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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130
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" or a region-specific format:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right">reference sequence, start, end, sample name, copy </span>number"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <span class="idiff left right">seq_name start end sample_name copy_</span>number"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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132
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ... for each region in each sample which does not have the"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" default copy number as set by --ploidy."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" default copy number as set by --ploidy. These fields can be delimited"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" by space or tab."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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134
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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135
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"output:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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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="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,6 +143,10 @@ void Parameters::usage(char** argv) {</td>
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139
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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Write gVCF output, which indicates coverage in uncalled regions."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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140
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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --gvcf-chunk NUM"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num 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">
141
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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" When writing gVCF output emit a record for every NUM bases."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -& --gvcf-dont-use-chunk BOOL "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" When writing the gVCF output emit a record for all bases if"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num new old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" set to </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">true</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> , will also route an int to --gvcf-chunk"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" similar to --output-mode EMIT_ALL_SITES from GATK"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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142
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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -@ --variant-input VCF"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Use variants reported in VCF file as input to the algorithm."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Variants in this file will included in the output even if"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="202" style="width: 35px; color: rgba(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">@@ -194,10 +202,6 @@ void Parameters::usage(char** argv) {</td>
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194
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<td class="diff-line-num new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"allele scope:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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196
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -I --no-snps Ignore SNP alleles."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -i --no-indels Ignore insertion and deletion alleles."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -u --no-complex Ignore complex events (composites of other classes)."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old_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">
201
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -n --use-best-n-alleles N"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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202
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Evaluate only the best N SNP alleles, ranked by sum of"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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203
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" supporting quality scores. (Set to 0 to use all; default: all)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -216,6 +220,23 @@ void Parameters::usage(char** argv) {</td>
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216
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" detection window. (default, use all observations, dividing partial"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old_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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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" support across matching haplotypes when generating haplotypes.)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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218
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" These flags are meant for testing."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" They are not meant for filtering the output."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" They actually filter the input to the algorithm by throwing away alignments."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" This hurts performance by hiding information from the Bayesian model."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Do not use them unless you can validate that they improve results!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -I --throw-away-snp-obs Remove SNP observations from input."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -i --throw-away-indels-obs Remove indel observations from input."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -X --throw-away-mnp-obs Remove MNP observations from input."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -u --throw-away-complex-obs Remove complex allele observations from input."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" If you need to break apart haplotype calls to obtain one class of alleles,"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" run the call with default parameters, then normalize and subset the VCF:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" freebayes ... | vcfallelicprimitives -kg >calls.vcf"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" For example, this would retain only biallelic SNPs."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <calls.vcf vcfsnps | vcfbiallelic >biallelic_snp_calls.vcf"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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219
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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"indel realignment:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
220
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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
221
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<td class="diff-line-num new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -O --dont-left-align-indels"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="297" style="width: 35px; color: rgba(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">@@ -276,8 +297,13 @@ void Parameters::usage(char** argv) {</td>
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276
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<td class="diff-line-num new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" to use the allele in analysis. default: 1"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
277
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<td class="diff-line-num new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --min-coverage N"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
278
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<td class="diff-line-num new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Require at least this coverage to process a site. default: 0"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="279" 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">
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="s" style="color: #d14;">" --max-coverage N"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Do not process sites with greater than this coverage. default: no limit"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --limit-coverage N"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num new old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Downsample per-sample coverage to this level if greater than this coverage."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" default: no limit"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -g --skip-coverage N"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Skip processing of alignments overlapping positions with coverage >N."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" This filters sites above this coverage, but will also reduce data nearby."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" default: no limit"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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281
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
282
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<td class="diff-line-num new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"population priors:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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283
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<td class="diff-line-num new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="414" style="width: 35px; color: rgba(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">@@ -388,6 +414,7 @@ Parameters::Parameters(int argc, char** argv) {</td>
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388
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">outputFile</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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389
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">gVCFout</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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390
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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;">gVCFchunk</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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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="n" style="color: #333;">gVCFNoChunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// --gvcf-no-chunk sets this to true</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;">alleleObservationBiasFile</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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392
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// operation parameters</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">@@ -461,7 +488,8 @@ Parameters::Parameters(int argc, char** argv) {</td>
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461
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> <span class="n" style="color: #333;">probContamination</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">10e-9</span><span class="p">;</span></span>
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462
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//minAltQSumTotal = 0;</span></span>
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463
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="cpp"> <span class="n" style="color: #333;">minCoverage</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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464
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="cpp"> <span class="n" style="color: #333;">maxCoverage</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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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">limitCoverage</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="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">skipCoverage</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="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">debuglevel</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="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">debug</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="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">debug2</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -486,6 +514,7 @@ Parameters::Parameters(int argc, char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"vcf"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'v'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gvcf"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'8'</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="p">{</span><span class="s" style="color: #d14;">"gvcf-chunk"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'&'</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="p">{</span><span class="s" style="color: #d14;">"gvcf-dont-use-chunk"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">,</span> <span class="sc" style="color: #d14;">'&'</span><span class="p">},</span></span>
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489
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"use-duplicate-reads"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'4'</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="p">{</span><span class="s" style="color: #d14;">"no-partial-observations"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'['</span><span class="p">},</span></span>
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491
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"use-best-n-alleles"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="507" style="width: 35px; color: rgba(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="536" style="width: 35px; color: rgba(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">@@ -507,15 +536,15 @@ Parameters::Parameters(int argc, char** argv) {</td>
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507
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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 class="s" style="color: #d14;">"read-max-mismatch-fraction"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'z'</span><span class="p">},</span></span>
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508
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"read-snp-limit"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'$'</span><span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
509
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"read-indel-limit"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'e'</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="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">no-indel</span>s"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">throw-away-indel-ob</span>s"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">},</span></span>
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511
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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="s" style="color: #d14;">"dont-left-align-indels"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'O'</span><span class="p">},</span></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">no-mnp</span>s"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">},</span></span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">no-complex</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'u'</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="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">throw-away-mnps-ob</span>s"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'X'</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="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">throw-away-complex-obs</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'u'</span><span class="p">},</span></span>
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514
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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 class="s" style="color: #d14;">"max-complex-gap"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'E'</span><span class="p">},</span></span>
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515
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"haplotype-length"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'E'</span><span class="p">},</span></span>
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516
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-repeat-size"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'E'</span><span class="p">},</span></span>
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517
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-repeat-entropy"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'E'</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="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">no-snp</span>s"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">},</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"<span class="idiff left right">throw-away-snp-ob</span>s"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">},</span></span>
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519
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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 class="s" style="color: #d14;">"indel-exclusion-window"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span></span>
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520
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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 class="s" style="color: #d14;">"theta"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'T'</span><span class="p">},</span></span>
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521
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"pvar"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="533" style="width: 35px; color: rgba(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="562" style="width: 35px; color: rgba(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">@@ -533,7 +562,8 @@ Parameters::Parameters(int argc, char** argv) {</td>
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533
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//{"min-alternate-mean-mapq", required_argument, 0, 'k'},</span></span>
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534
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-alternate-qsum"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'3'</span><span class="p">},</span></span>
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535
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"min-coverage"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'!'</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 class="s" style="color: #d14;">"max-coverage"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'+'</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="p">{</span><span class="s" style="color: #d14;">"limit-coverage"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'+'</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 class="s" style="color: #d14;">"skip-coverage"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">},</span></span>
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537
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"genotype-qualities"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'='</span><span class="p">},</span></span>
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538
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"variant-input"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'@'</span><span class="p">},</span></span>
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539
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"only-use-input-alleles"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="589" style="width: 35px; color: rgba(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">@@ -559,7 +589,7 @@ Parameters::Parameters(int argc, char** argv) {</td>
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559
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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;">while</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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560
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="cpp"></span>
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561
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">option_index</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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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</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="s" style="color: #d14;">"hcO4ZKjH[0diN5a)Ik=wl6#uVXJY:b:G:M:x:@:A:f:t:r:s:v:n:B:p:m:q:R:Q:U:$:e:T:P:D:^:S:W:F:C:&:L:8z:1:3:E:7:2:9:%:_:,:(:!:+:"</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="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</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="s" style="color: #d14;">"hcO4ZKjH[0diN5a)Ik=wl6#uVXJY:b:G:M:x:@:A:f:t:r:s:v:n:B:p:m:q:R:Q:U:$:e:T:P:D:^:S:W:F:C:&:L:8z:1:3:E:7:2:9:%:_:,:(:!:+:<span class="idiff left right">g:</span>"</span><span class="p">,</span></span>
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563
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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;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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564
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC595" 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="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="c1" style="color: #998; font-style: italic;">// end of options</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">@@ -635,8 +665,16 @@ Parameters::Parameters(int argc, char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">gVCFout</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="LC666" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -& BOOL/INT --gvcf-no-chunk BOOL/INT --gvcf-chunk </span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'&'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">gVCFchunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//cerr << "optarg:\t" << optarg << endl;</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;">optarg</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="sc" style="color: #d14;">'t'</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="n" style="color: #333;">gVCFNoChunk</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="LC673" 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;">optarg</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="sc" style="color: #d14;">'f'</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="n" style="color: #333;">gVCFNoChunk</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="LC675" 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="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">gVCFchunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span> </span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -4 --use-duplicate-reads</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -668,10 +706,18 @@ Parameters::Parameters(int argc, char** argv) {</td>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -+ --<span class="idiff left right">max</span>-coverage</span></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -+ --<span class="idiff left right">limit</span>-coverage</span></span>
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672
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'+'</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="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;">convert</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="n" style="color: #333;">maxCoverage</span><span class="p">))</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="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"could not parse max-coverage"</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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711
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<pre style="margin: 0;">+<span id="LC711" 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;">convert</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="n" style="color: #333;">limitCoverage</span><span class="p">))</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"could not parse limit-coverage"</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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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <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;">break</span><span class="p">;</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -g --skip-coverage</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'g'</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="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;">convert</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="n" style="color: #333;">skipCoverage</span><span class="p">))</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"could not parse skip-coverage"</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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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</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="LC722" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#59d68511ee53779f7d3986f01f6c076fc94153fa"><strong>src/Parameters.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">@@ -37,6 +37,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">outputFile</span><span class="p">;</span></span>
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38
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gVCFout</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -l --gvcf</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gVCFchunk</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gVCFNoChunk</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">variantPriorsFile</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">haplotypeVariantFile</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">reportAllHaplotypeAlleles</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">@@ -120,7 +121,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minAltCount</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -C --min-alternate-count</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minAltTotal</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -G --min-alternate-total</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minCoverage</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -! --min-coverage</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxCoverage</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -+ --max-coverage</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limitCoverage</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -+ --limit-coverage</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">skipCoverage</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -g --skip-coverage</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">debuglevel</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// -d --debug increments</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">debug</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// set if debuglevel >=1</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">debug2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// set if debuglevel >=2</span></span>
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<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#96880c749ae3f3b78a514158e074cbee415d97f4"><strong>src/ResultData.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">@@ -656,7 +656,10 @@ vcflib::Variant& Results::gvcf(</td>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"> <span class="n" style="color: #333;">endPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">currentPosition</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">numSites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endPos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">startPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">numSites</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="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numSites</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="LC660" 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;">"Hit end of chr, but still attempted to call location !!! </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> Breaking</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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<pre style="margin: 0;">+<span id="LC661" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set up site call</span></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">referenceSubstr</span><span class="p">(</span><span class="n" style="color: #333;">startPos</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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">@@ -673,17 +676,15 @@ vcflib::Variant& Results::gvcf(</td>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"DP"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"MIN_DP"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"QR"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"RO"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"QA"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"AO"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp"> <span class="n" style="color: #333;">NonCall</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">aggregateAll</span><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="cm" style="color: #998; font-style: italic;">/* This resets min depth to zero if nonCalls is less than numSites. */</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minDepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">minDepth</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="cpp"></span>
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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;">numSites</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">nCount</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;">minDepth</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="LC686" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minDepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">numSites</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">nCount</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">minDepth</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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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"DP"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">((</span><span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">refCount</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">total</span><span class="p">.</span><span class="n" style="color: #333;">altCount</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">numSites</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"MIN_DP"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">minDepth</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">@@ -707,17 +708,16 @@ vcflib::Variant& Results::gvcf(</td>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* This resets min depth to zero if nonCalls is less than numSites. */</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minDepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">minDepth</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">numSites</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">nCount</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">minDepth</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="LC715" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minDepth</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">numSites</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">nCount</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">minDepth</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp"> <span class="n" style="color: #333;">sampleOutput</span><span class="p">[</span><span class="s" style="color: #d14;">"DP"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">((</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">refCount</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">altCount</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">numSites</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="n" style="color: #333;">sampleOutput</span><span class="p">[</span><span class="s" style="color: #d14;">"MIN_DP"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">minDepth</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp"> <span class="n" style="color: #333;">sampleOutput</span><span class="p">[</span><span class="s" style="color: #d14;">"QR"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">ln2phred</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">reflnQ</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 class="n" style="color: #333;">sampleOutput</span><span class="p">[</span><span class="s" style="color: #d14;">"RO"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">((</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">refCount</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">numSites</span><span class="p">)));</span></span>
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720
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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;">sampleOutput</span><span class="p">[</span><span class="s" style="color: #d14;">"QA"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">(</span><span class="n" style="color: #333;">ln2phred</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">altlnQ</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;">sampleOutput</span><span class="p">[</span><span class="s" style="color: #d14;">"AO"</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">convert</span><span class="p">((</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">altCount</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">numSites</span><span class="p">)));</span></span>
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721
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"> <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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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">var</span><span class="p">;</span></span>
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<li id="0a8324dd44ff9732a3b3dab3603558762809dc6c">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#0a8324dd44ff9732a3b3dab3603558762809dc6c"><strong>src/freebayes.cpp</strong></a>
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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>
<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,7 +106,7 @@ int main (int argc, char *argv[]) {</td>
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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">variantCallFile</span><span class="p">.</span><span class="n" style="color: #333;">header</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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107
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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>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"></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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>Coverage</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">limit</span>Coverage</span><span class="p">)</span> <span class="p">{</span></span>
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110
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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;">srand</span><span class="p">(</span><span class="mi" style="color: #099;">13</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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112
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<pre style="margin: 0;"> <span id="LC112" 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">@@ -120,15 +120,19 @@ int main (int argc, char *argv[]) {</td>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">total_sites</span><span class="p">;</span></span>
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121
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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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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG2</span><span class="p">(</span><span class="s" style="color: #d14;">"at start of main loop"</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>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// did we switch chromosomes or exceed our gVCF chunk size?</span></span>
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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;">// did we switch chromosomes or exceed our gVCF chunk size<span class="idiff left right">, or do we not want to use chunks</span>?</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if so, we may need to output a gVCF record</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">Results</span> <span class="n" style="color: #333;">results</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFout</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp"> <span class="p">(</span> <span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">currentSequenceName</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFchunk</span> <span class="o" style="font-weight: 600;">&&</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">lastPos</span><span class="p">().</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">firstPos</span><span class="p">().</span><span class="n" style="color: #333;">second</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFchunk</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFout</span> </span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> </span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFNoChunk</span><span class="p">)</span></span>
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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="p">(</span><span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">currentSequenceName</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFchunk</span> </span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">lastPos</span><span class="p">().</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">firstPos</span><span class="p">().</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFchunk</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">vcflib</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">var</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">variantCallFile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">gvcf</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">nonCalls</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">clear</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">@@ -157,7 +161,7 @@ int main (int argc, char *argv[]) {</td>
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157
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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 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;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">onlyUseInputAlleles</span><span class="p">)</span> <span class="p">{</span></span>
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158
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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;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"no input alleles, but using only input alleles for analysis, skipping position"</span><span class="p">);</span></span>
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159
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">skip</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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160
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<pre style="margin: 0;">-<span id="LC160" 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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>Coverage</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="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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">limit</span>Coverage</span><span class="p">)</span> <span class="p">{</span></span>
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161
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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;">// go through each sample</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;">for</span> <span class="p">(</span><span class="n" style="color: #333;">Samples</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</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;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">s</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;">end</span><span class="p">();</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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163
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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;">string</span> <span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -167,14 +171,14 @@ int main (int argc, char *argv[]) {</td>
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167
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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;">Sample</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">sg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">sg</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample</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;">sg</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="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">sampleCoverage</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sg</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>
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169
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<pre style="margin: 0;"> <span id="LC173" 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;">sampleCoverage</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>Coverage</span><span class="p">)</span> <span class="p">{</span></span>
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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;">sampleCoverage</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">limit</span>Coverage</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="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>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"coverage "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sampleCoverage</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for sample "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" was > "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">maxCoverage</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">", so we will remove "</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">sampleCoverage</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">parameters</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">max</span>Coverage</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" genotypes"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">DEBUG</span><span class="p">(</span><span class="s" style="color: #d14;">"coverage "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sampleCoverage</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for sample "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sampleName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" was > "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">limitCoverage</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">", so we will remove "</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">sampleCoverage</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">parameters</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">limit</span>Coverage</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" genotypes"</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="n" style="color: #333;">vector</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;">genotypesToErase</span><span class="p">;</span></span>
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176
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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;">do</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probRemove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sampleCoverage</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>Coverage</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;">sampleCoverage</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probRemove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sampleCoverage</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">limit</span>Coverage</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;">sampleCoverage</span><span class="p">;</span></span>
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178
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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;">vector</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;">genotypesToErase</span><span class="p">;</span></span>
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179
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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;">// iterate through the genotypes</span></span>
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180
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">Sample</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">sg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">sg</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample</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;">sg</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="186" style="width: 35px; color: rgba(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">@@ -182,7 +186,7 @@ int main (int argc, char *argv[]) {</td>
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182
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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;">// iterate through each allele</span></span>
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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;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alleleIndex</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;">alleleIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sg</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="n" style="color: #333;">alleleIndex</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</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="c1" style="color: #998; font-style: italic;">// only if we have more alleles to remove</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>Coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sampleCoverage</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">limit</span>Coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sampleCoverage</span><span class="p">)</span> <span class="p">{</span></span>
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186
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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;">double</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rand</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;">RAND_MAX</span><span class="p">;</span></span>
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187
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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;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">probRemove</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// skip over this allele</span></span>
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188
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">sampleCoverage</span><span class="o" style="font-weight: 600;">--</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">@@ -205,7 +209,7 @@ int main (int argc, char *argv[]) {</td>
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205
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</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;">iterator</span> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genotypesToErase</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">genotypesToErase</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;">gt</span><span class="p">)</span> <span class="p">{</span></span>
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206
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gt</span><span class="p">);</span></span>
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207
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211
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<pre style="margin: 0;"> <span id="LC211" 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 class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">max</span>Coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sampleCoverage</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="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">limit</span>Coverage</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sampleCoverage</span><span class="p">);</span></span>
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209
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">sampleCoverage</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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210
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">Sample</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">sg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">sg</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">sample</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;">sg</span><span class="p">)</span> <span class="p">{</span></span>
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211
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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;">sampleCoverage</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sg</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>
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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">@@ -679,7 +683,8 @@ int main (int argc, char *argv[]) {</td>
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679
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp"> <span class="p">}</span></span>
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680
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp"></span>
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681
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// write the last gVCF record</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;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFout</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">nonCalls</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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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// NOTE: for some resion this is only needed if we are using gVCF chunks, if minimal chunking it is not requird, in fact it breaks....</span></span>
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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;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFout</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">nonCalls</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">gVCFNoChunk</span><span class="p">)</span> <span class="p">{</span></span>
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683
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688
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp"> <span class="n" style="color: #333;">Results</span> <span class="n" style="color: #333;">results</span><span class="p">;</span></span>
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684
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689
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">vcflib</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">var</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">variantCallFile</span><span class="p">);</span></span>
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685
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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;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">gvcf</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">nonCalls</span><span class="p">,</span> <span class="n" style="color: #333;">parser</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<li id="b512495eaf318bcd937a386870aed8d1e50a1b0d">
<a href="https://salsa.debian.org/med-team/freebayes/compare/e25d5f67541ce352be9c5106b29296a5ee4ef049...7dcb2b38a2878deadf144ddd994774a11ff2b342#b512495eaf318bcd937a386870aed8d1e50a1b0d"><strong>test/t/01_call_variants.t</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">@@ -7,7 +7,7 @@ PATH=../bin:$PATH # for freebayes</td>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=../</span><span class="nv" style="color: #008080;">scripts:$PATH</span> <span class="c1" style="color: #998; font-style: italic;"># for freebayes-parallel</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=..</span><span class="sr" style="color: #009926;">/vcflib/</span><span class="nv" style="color: #008080;">bin:$PATH</span> <span class="c1" style="color: #998; font-style: italic;"># for vcf binaries used by freebayes-parallel</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="perl"><span class="nv" style="color: #008080;">plan</span> <span class="nv" style="color: #008080;">tests</span> <span class="mi" style="color: #099;">2<span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="nv" style="color: #008080;">plan</span> <span class="nv" style="color: #008080;">tests</span> <span class="mi" style="color: #099;">2<span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"><span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="nv" style="color: #008080;">echo</span> <span class="p">"</span><span class="s2" style="color: #d14;">$(comm -12 <(cat tiny/NA12878.chr22.tiny.giab.vcf | grep -v </span><span class="p">"</span><span class="o" style="font-weight: 600;">^</span><span class="c1" style="color: #998; font-style: italic;">#" | cut -f 2 | sort) <(freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam | grep -v "^#" | cut -f 2 | sort) | wc -l) >= 13" | bc) 1 "variant calling recovers most of the GiAB variants in a test region"</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"></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">@@ -111,8 +111,13 @@ is $(freebayes -f splice/1:883884-887618.fa splice/1:883884-887618.bam -F 0.05 -</td>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="perl"><span class="sx" style="color: #d14;">is $(freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam --gvcf | grep '<\*>' | wc -l) 20 "freebayes produces the expected number of lines of gVCF output"</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="perl"><span class="sx" style="color: #d14;">is $(freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam --gvcf --gvcf-chunk 50 | grep '<\*>' | wc -l) 245 "freebayes produces the expected number of lines of gVCF output"</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="perl"><span class="sx" style="color: #d14;">is $(freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam --gvcf --gvcf-chunk 50 | grep '<\*>' | wc -l) 250 "freebayes produces the expected number of lines of gVCF output"</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="perl"><span class="sx" style="color: #d14;">is $(freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam --gvcf --gvcf-dont-use-chunk true | grep '<\*>' | wc -l) 12250 "freebayes produces the expected number of lines of gVCF output"</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"><span class="sx" style="color: #d14;">samtools view -h tiny/NA12878.chr22.tiny.bam | sed s/NA12878D_</span><span class="nv" style="color: #008080;">HiSeqX_R1</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">fastq</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">gz</span><span class="sr" style="color: #009926;">/222.NA12878D_HiSeqX_R1.fastq.gz/</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">sed</span> <span class="sr" style="color: #009926;">s/SM:1/SM:2/</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">sam</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="perl"><span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="nv" style="color: #008080;">freebayes</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">f</span> <span class="nv" style="color: #008080;">tiny</span><span class="sr" style="color: #009926;">/q.fa -F 0.2 tiny/</span><span class="nv" style="color: #008080;">NA12878</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">chr22</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">tiny</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">bam</span> <span class="nv" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">sam</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">A</span> <span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="nv" style="color: #008080;">echo</span> <span class="mi" style="color: #099;">1</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span> <span class="nv" style="color: #008080;">echo</span> <span class="mi" style="color: #099;">2</span> <span class="mi" style="color: #099;">13</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="p">'</span><span class="s1" style="color: #d14;">AN=21</span><span class="p">'</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">wc</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">l</span><span class="p">)</span> <span class="mi" style="color: #099;">19</span> <span class="p">"</span><span class="s2" style="color: #d14;">the CNV map may be used to specify per-sample copy numbers</span><span class="p">"</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="perl"><span class="nv" style="color: #008080;">rm</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">f</span> <span class="nv" style="color: #008080;">x</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">sam</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="perl"><span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="nv" style="color: #008080;">freebayes</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">f</span> <span class="nv" style="color: #008080;">tiny</span><span class="sr" style="color: #009926;">/q.fa --skip-coverage 30 tiny/</span><span class="nv" style="color: #008080;">NA12878</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">chr22</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">tiny</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">bam</span> <span class="o" style="font-weight: 600;">|</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">v</span> <span class="p">'</span><span class="s1" style="color: #d14;">^#</span><span class="p">'</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">wc</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">l</span><span class="p">)</span> <span class="mi" style="color: #099;">22</span> <span class="p">"</span><span class="s2" style="color: #d14;">freebayes makes the expected number of calls when capping coverage</span><span class="p">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="perl"><span class="nv" style="color: #008080;">is</span> <span class="nv" style="color: #008080;">$</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="nv" style="color: #008080;">freebayes</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">f</span> <span class="nv" style="color: #008080;">tiny</span><span class="sr" style="color: #009926;">/q.fa -g 30 tiny/</span><span class="nv" style="color: #008080;">NA12878</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">chr22</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">tiny</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">bam</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">vcfkeepinfo</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">DP</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">vcf2tsv</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">cut</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">f</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">tail</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">n</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="nv" style="color: #008080;">awk</span> <span class="p">'</span><span class="s1" style="color: #d14;">$1 <= 30 { print }</span><span class="p">'</span> <span class="o" style="font-weight: 600;">|</span> <span class="nv" style="color: #008080;">wc</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">l</span><span class="p">)</span> <span class="mi" style="color: #099;">22</span> <span class="p">"</span><span class="s2" style="color: #d14;">all coverage capped calls are below the coverage threshold</span><span class="p">"</span></span></pre>
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